[ Started: 2022-05-04 12:00:36 ] cli (3.2.0 -> 3.3.0 ) [CRAN] tibble (3.1.6 -> 3.1.7 ) [CRAN] ggplot2 (3.3.5 -> 3.3.6 ) [CRAN] BiocParallel (1.29.21 -> 1.30.0 ) [CRAN] limma (3.51.8 -> 3.52.0 ) [CRAN] ps (1.6.0 -> 1.7.0 ) [CRAN] zlibbioc (1.41.0 -> 1.42.0 ) [CRAN] GenomeInfoDb (1.31.7 -> 1.32.1 ) [CRAN] XVector (0.35.0 -> 0.36.0 ) [CRAN] Biostrings (2.63.3 -> 2.64.0 ) [CRAN] httr (1.4.2 -> 1.4.3 ) [CRAN] KEGGREST (1.35.0 -> 1.36.0 ) [CRAN] S4Vectors (0.33.17 -> 0.34.0 ) [CRAN] RSQLite (2.2.12 -> 2.2.13 ) [CRAN] IRanges (2.29.1 -> 2.30.0 ) [CRAN] Biobase (2.55.2 -> 2.56.0 ) [CRAN] BiocGenerics (0.41.2 -> 0.42.0 ) [CRAN] Annotatio... (1.57.1 -> 1.58.0 ) [CRAN] knitr (1.38 -> 1.39 ) [CRAN] dplyr (1.0.8 -> 1.0.9 ) [CRAN] fgsea (1.21.2 -> 1.22.0 ) [CRAN] marray (1.73.0 -> 1.74.0 ) [CRAN] gplots (3.1.1 -> 3.1.3 ) [CRAN] graph (1.73.0 -> 1.74.0 ) [CRAN] annotate (1.73.0 -> 1.74.0 ) [CRAN] viper (1.29.0 -> 1.30.0 ) [CRAN] bcellViper (1.31.0 -> 1.32.0 ) [CRAN] rmarkdown (2.13 -> 2.14 ) [CRAN] piano (2.11.2 -> 2.12.0 ) [CRAN] testthat (3.1.3 -> 3.1.4 ) [CRAN] GSEABase (1.57.0 -> 1.58.0 ) [CRAN] CARNIVAL (14057d13a... -> 8b3f0dff8...) [GitHub] Installing 31 packages: cli, tibble, ggplot2, BiocParallel, limma, ps, zlibbioc, GenomeInfoDb, XVector, Biostrings, httr, KEGGREST, S4Vectors, RSQLite, IRanges, Biobase, BiocGenerics, AnnotationDbi, knitr, dplyr, fgsea, marray, gplots, graph, annotate, viper, bcellViper, rmarkdown, piano, testthat, GSEABase trying URL 'https://cloud.r-project.org/src/contrib/cli_3.3.0.tar.gz' Content type 'application/x-gzip' length 495823 bytes (484 KB) ================================================== downloaded 484 KB trying URL 'https://cloud.r-project.org/src/contrib/tibble_3.1.7.tar.gz' Content type 'application/x-gzip' length 674873 bytes (659 KB) ================================================== downloaded 659 KB trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.3.6.tar.gz' Content type 'application/x-gzip' length 3061989 bytes (2.9 MB) ================================================== downloaded 2.9 MB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/BiocParallel_1.30.0.tar.gz' Content type 'application/x-gzip' length 897235 bytes (876 KB) ================================================== downloaded 876 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/limma_3.52.0.tar.gz' Content type 'application/x-gzip' length 1513449 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://cloud.r-project.org/src/contrib/ps_1.7.0.tar.gz' Content type 'application/x-gzip' length 125455 bytes (122 KB) ================================================== downloaded 122 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/zlibbioc_1.42.0.tar.gz' Content type 'application/x-gzip' length 214249 bytes (209 KB) ================================================== downloaded 209 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/GenomeInfoDb_1.32.1.tar.gz' Content type 'application/x-gzip' length 3452862 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/XVector_0.36.0.tar.gz' Content type 'application/x-gzip' length 67787 bytes (66 KB) ================================================== downloaded 66 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Biostrings_2.64.0.tar.gz' Content type 'application/x-gzip' length 12424145 bytes (11.8 MB) ================================================== downloaded 11.8 MB trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.3.tar.gz' Content type 'application/x-gzip' length 161122 bytes (157 KB) ================================================== downloaded 157 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/KEGGREST_1.36.0.tar.gz' Content type 'application/x-gzip' length 25777 bytes (25 KB) ================================================== downloaded 25 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/S4Vectors_0.34.0.tar.gz' Content type 'application/x-gzip' length 618611 bytes (604 KB) ================================================== downloaded 604 KB trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.2.13.tar.gz' Content type 'application/x-gzip' length 3683702 bytes (3.5 MB) ================================================== downloaded 3.5 MB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/IRanges_2.30.0.tar.gz' Content type 'application/x-gzip' length 455708 bytes (445 KB) ================================================== downloaded 445 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Biobase_2.56.0.tar.gz' Content type 'application/x-gzip' length 1551809 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/BiocGenerics_0.42.0.tar.gz' Content type 'application/x-gzip' length 45966 bytes (44 KB) ================================================== downloaded 44 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/AnnotationDbi_1.58.0.tar.gz' Content type 'application/x-gzip' length 4329159 bytes (4.1 MB) ================================================== downloaded 4.1 MB trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.39.tar.gz' Content type 'application/x-gzip' length 898418 bytes (877 KB) ================================================== downloaded 877 KB trying URL 'https://cloud.r-project.org/src/contrib/dplyr_1.0.9.tar.gz' Content type 'application/x-gzip' length 957637 bytes (935 KB) ================================================== downloaded 935 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/fgsea_1.22.0.tar.gz' Content type 'application/x-gzip' length 1274597 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/marray_1.74.0.tar.gz' Content type 'application/x-gzip' length 5043596 bytes (4.8 MB) ================================================== downloaded 4.8 MB trying URL 'https://cloud.r-project.org/src/contrib/gplots_3.1.3.tar.gz' Content type 'application/x-gzip' length 520683 bytes (508 KB) ================================================== downloaded 508 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/graph_1.74.0.tar.gz' Content type 'application/x-gzip' length 713157 bytes (696 KB) ================================================== downloaded 696 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/annotate_1.74.0.tar.gz' Content type 'application/x-gzip' length 1472975 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/viper_1.30.0.tar.gz' Content type 'application/x-gzip' length 314905 bytes (307 KB) ================================================== downloaded 307 KB trying URL 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/bcellViper_1.32.0.tar.gz' Content type 'application/x-gzip' length 11785648 bytes (11.2 MB) ================================================== downloaded 11.2 MB trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.14.tar.gz' Content type 'application/x-gzip' length 3241807 bytes (3.1 MB) ================================================== downloaded 3.1 MB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/piano_2.12.0.tar.gz' Content type 'application/x-gzip' length 1599346 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cloud.r-project.org/src/contrib/testthat_3.1.4.tar.gz' Content type 'application/x-gzip' length 700919 bytes (684 KB) ================================================== downloaded 684 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/GSEABase_1.58.0.tar.gz' Content type 'application/x-gzip' length 241149 bytes (235 KB) ================================================== downloaded 235 KB * installing *source* package ‘cli’ ... ** package ‘cli’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c ansi.c -o ansi.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c cleancall.c -o cleancall.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c diff.c -o diff.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c errors.c -o errors.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c md5.c -o md5.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress-altrep.c -o progress-altrep.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress.c -o progress.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c sha256.c -o sha256.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c thread.c -o thread.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c tty.c -o tty.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c utf8.c -o utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c win-utf8.c -o win-utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c winfiles.c -o winfiles.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o init.o md5.o progress-altrep.o progress.o sha256.o thread.o tty.o utf8.o win-utf8.o winfiles.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-cli/00new/cli/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cli) * installing *source* package ‘tibble’ ... ** package ‘tibble’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c attributes.c -o attributes.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c coerce.c -o coerce.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c matrixToDataFrame.c -o matrixToDataFrame.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o tibble.so attributes.o coerce.o init.o matrixToDataFrame.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-tibble/00new/tibble/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tibble) * installing *source* package ‘BiocParallel’ ... ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for shm_open in -lrt... yes configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/BH/include' -I/usr/local/include -fpic -Wall -pedantic -c ipcmutex.cpp -o ipcmutex.o In file included from /opt/R-rc/lib/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/arg.hpp:25, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/apply.hpp:24, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/fold.hpp:20, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/remove_if.hpp:18, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/remove.hpp:18, from /opt/R-rc/lib/R/library/BH/include/boost/function_types/components.hpp:44, from /opt/R-rc/lib/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14, from /opt/R-rc/lib/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10, from /opt/R-rc/lib/R/library/BH/include/boost/tti/has_member_function.hpp:15, from /opt/R-rc/lib/R/library/BH/include/boost/uuid/random_generator.hpp:20, from /opt/R-rc/lib/R/library/BH/include/boost/uuid/uuid_generators.hpp:17, from ipcmutex.cpp:3: /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -lrt -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-BiocParallel/00new/BiocParallel/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocParallel) * installing *source* package ‘limma’ ... ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c normexp.c -o normexp.o normexp.c: In function ‘fit_saddle_nelder_mead’: normexp.c:165:78: warning: ISO C forbids passing argument 9 of ‘nmmin’ between function pointer and ‘void *’ [-Wpedantic] 165 | nmmin(3, par, parsOut, Fmin, normexp_m2loglik_saddle, fail, abstol, intol, &ex, alpha, beta, gamma, trace, fncount, maxit); | ^~~ In file included from normexp.c:12: /opt/R-rc/lib/R/include/R_ext/Applic.h:73:51: note: expected ‘void *’ but argument is of type ‘void (*)()’ 73 | int *fail, double abstol, double intol, void *ex, | ~~~~~~^~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-limma/00new/limma/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (limma) * installing *source* package ‘ps’ ... ** package ‘ps’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -std=gnu99 -Wall -pedantic -L/usr/local/lib -Wall px.c -o px gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c api-common.c -o api-common.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c common.c -o common.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c extra.c -o extra.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c dummy.c -o dummy.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c error-codes.c -o error-codes.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c posix.c -o posix.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c api-posix.c -o api-posix.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c linux.c -o linux.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c api-linux.c -o api-linux.o api-linux.c: In function ‘psll_get_cpu_aff’: api-linux.c:1139:9: warning: ‘pid’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1139 | if (sched_getaffinity(pid, setsize, mask) == 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o ps.so init.o api-common.o common.o extra.o dummy.o error-codes.o posix.o api-posix.o linux.o api-linux.o -L/opt/R-rc/lib/R/lib -lR installing via 'install.libs.R' to /home/omnipath/local/R/00LOCK-ps/00new/ps ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ps) * installing *source* package ‘zlibbioc’ ... ** using staged installation configure: creating ./config.status config.status: creating src/Makevars ** libs mkdir -p "/home/omnipath/local/R/00LOCK-zlibbioc/00new/zlibbioc/include" gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c R_init_zlibbioc.c -o R_init_zlibbioc.o R_init_zlibbioc.c:1: warning: ISO C forbids an empty translation unit [-Wpedantic] 1 | /* do not remove */ | gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o zlibbioc.so R_init_zlibbioc.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-zlibbioc/00new/zlibbioc/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (zlibbioc) * installing *source* package ‘httr’ ... ** package ‘httr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (httr) * installing *source* package ‘RSQLite’ ... ** package ‘RSQLite’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c DbColumn.cpp -o DbColumn.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from DbColumn.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c DbColumnDataSource.cpp -o DbColumnDataSource.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from DbColumnDataSource.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c DbColumnDataSourceFactory.cpp -o DbColumnDataSourceFactory.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from DbColumnDataSourceFactory.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c DbColumnStorage.cpp -o DbColumnStorage.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from DbColumnStorage.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c DbConnection.cpp -o DbConnection.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from DbConnection.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c DbDataFrame.cpp -o DbDataFrame.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from DbDataFrame.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from vendor/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from vendor/boost/smart_ptr/detail/yield_k.hpp:23, from vendor/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from vendor/boost/smart_ptr/detail/spinlock.hpp:42, from vendor/boost/smart_ptr/detail/spinlock_pool.hpp:25, from vendor/boost/smart_ptr/shared_ptr.hpp:29, from vendor/boost/shared_ptr.hpp:17, from DbColumn.h:7, from DbDataFrame.cpp:3: vendor/boost/config/pragma_message.hpp:24:34: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ vendor/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’ 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c DbResult.cpp -o DbResult.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from DbResult.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c RcppExports.cpp -o RcppExports.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from RSQLite_types.h:1, from RcppExports.cpp:4: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c SqliteColumnDataSource.cpp -o SqliteColumnDataSource.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from SqliteColumnDataSource.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c SqliteColumnDataSourceFactory.cpp -o SqliteColumnDataSourceFactory.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from SqliteColumnDataSourceFactory.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c SqliteDataFrame.cpp -o SqliteDataFrame.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from SqliteDataFrame.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c SqliteResult.cpp -o SqliteResult.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from SqliteResult.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c SqliteResultImpl.cpp -o SqliteResultImpl.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from SqliteResultImpl.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -std=gnu99 -Wall -pedantic -c affinity.c -o affinity.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c connection.cpp -o connection.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from connection.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -std=gnu99 -Wall -pedantic -c ext-csv.c -o ext-csv.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -std=gnu99 -Wall -pedantic -c ext-math.c -o ext-math.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -std=gnu99 -Wall -pedantic -c ext-regexp.c -o ext-regexp.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -std=gnu99 -Wall -pedantic -c ext-series.c -o ext-series.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c extensions.cpp -o extensions.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from extensions.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -std=gnu99 -Wall -pedantic -c import-file.c -o import-file.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c result.cpp -o result.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from result.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -Wall -pedantic -c rsqlite.cpp -o rsqlite.o In file included from vendor/boost/mpl/aux_/na_assert.hpp:23, from vendor/boost/mpl/arg.hpp:25, from vendor/boost/mpl/placeholders.hpp:24, from vendor/boost/iterator/iterator_categories.hpp:16, from vendor/boost/iterator/iterator_concepts.hpp:10, from vendor/boost/range/concepts.hpp:20, from vendor/boost/range/size_type.hpp:20, from vendor/boost/range/size.hpp:21, from vendor/boost/range/functions.hpp:20, from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp:30, from vendor/boost/ptr_container/ptr_sequence_adapter.hpp:20, from vendor/boost/ptr_container/ptr_vector.hpp:20, from RSQLite.h:15, from pch.h:1, from rsqlite.cpp:1: vendor/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ vendor/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/opt/R-rc/lib/R/library/plogr/include' -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -std=gnu99 -Wall -pedantic -c vendor/sqlite3/sqlite3.c -o vendor/sqlite3/sqlite3.o g++ -std=gnu++14 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o RSQLite.so DbColumn.o DbColumnDataSource.o DbColumnDataSourceFactory.o DbColumnStorage.o DbConnection.o DbDataFrame.o DbResult.o RcppExports.o SqliteColumnDataSource.o SqliteColumnDataSourceFactory.o SqliteDataFrame.o SqliteResult.o SqliteResultImpl.o affinity.o connection.o ext-csv.o ext-math.o ext-regexp.o ext-series.o extensions.o import-file.o result.o rsqlite.o vendor/sqlite3/sqlite3.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-RSQLite/00new/RSQLite/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RSQLite) * installing *source* package ‘BiocGenerics’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’ Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ Creating a new generic function for ‘get’ in package ‘BiocGenerics’ Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ Creating a new generic function for ‘grep’ in package ‘BiocGenerics’ Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’ Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘match’ in package ‘BiocGenerics’ Creating a new generic function for ‘order’ in package ‘BiocGenerics’ Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ Creating a new generic function for ‘union’ in package ‘BiocGenerics’ Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’ Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’ Creating a new generic function for ‘sort’ in package ‘BiocGenerics’ Creating a new generic function for ‘table’ in package ‘BiocGenerics’ Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’ Creating a new generic function for ‘var’ in package ‘BiocGenerics’ Creating a new generic function for ‘sd’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’ Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’ Creating a new generic function for ‘mad’ in package ‘BiocGenerics’ Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ Creating a new generic function for ‘basename’ in package ‘BiocGenerics’ Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocGenerics) * installing *source* package ‘knitr’ ... ** package ‘knitr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (knitr) * installing *source* package ‘gplots’ ... ** package ‘gplots’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gplots) * installing *source* package ‘ggplot2’ ... ** package ‘ggplot2’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggplot2) * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c AEbufs.c -o AEbufs.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c DataFrame_class.c -o DataFrame_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c Hits_class.c -o Hits_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c LLint_class.c -o LLint_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c List_class.c -o List_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c Rle_class.c -o Rle_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c Rle_utils.c -o Rle_utils.o Rle_utils.c: In function ‘Rle_real_runq’: Rle_utils.c:701:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 701 | if (count_na != 0) | ^~ Rle_utils.c:703:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 703 | q_index = roundingScale(window_len_na, | ^~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c SEXP_utils.c -o SEXP_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c SimpleList_class.c -o SimpleList_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c anyMissing.c -o anyMissing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c character_utils.c -o character_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c eval_utils.c -o eval_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c hash_utils.c -o hash_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c integer_utils.c -o integer_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c logical_utils.c -o logical_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c raw_utils.c -o raw_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c safe_arithm.c -o safe_arithm.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c sort_utils.c -o sort_utils.o sort_utils.c:263:13: warning: ‘sort_uchar_array’ defined but not used [-Wunused-function] 263 | static void sort_uchar_array(unsigned char *x, int nelt, int desc) | ^~~~~~~~~~~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c subsetting_utils.c -o subsetting_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c vector_utils.c -o vector_utils.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List” Creating a new generic function for ‘unname’ in package ‘S4Vectors’ Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’ Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’ Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame” Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table” Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (S4Vectors) * installing *source* package ‘Biobase’ ... ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c Rinit.c -o Rinit.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c anyMissing.c -o anyMissing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c envir.c -o envir.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c matchpt.c -o matchpt.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c rowMedians.c -o rowMedians.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c sublist_extract.c -o sublist_extract.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-Biobase/00new/Biobase/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Biobase) * installing *source* package ‘dplyr’ ... ** package ‘dplyr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c chop.cpp -o chop.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c filter.cpp -o filter.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c funs.cpp -o funs.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c group_by.cpp -o group_by.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c group_data.cpp -o group_data.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c imports.cpp -o imports.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c init.cpp -o init.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c mask.cpp -o mask.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c mutate.cpp -o mutate.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c slice.cpp -o slice.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c summarise.cpp -o summarise.o g++ -std=gnu++14 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-dplyr/00new/dplyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dplyr) * installing *source* package ‘marray’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (marray) * installing *source* package ‘graph’ ... ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c graph.c -o graph.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o graph.so graph.o -L/opt/R-rc/lib/R/lib -lR mv graph.so BioC_graph.so installing to /home/omnipath/local/R/00LOCK-graph/00new/graph/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graph) * installing *source* package ‘rmarkdown’ ... ** package ‘rmarkdown’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rmarkdown) * installing *source* package ‘testthat’ ... ** package ‘testthat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c reassign.c -o reassign.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -Wall -pedantic -c test-catch.cpp -o test-catch.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -Wall -pedantic -c test-example.cpp -o test-example.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -Wall -pedantic -c test-runner.cpp -o test-runner.o g++ -std=gnu++14 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o testthat.so init.o reassign.o test-catch.o test-example.o test-runner.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-testthat/00new/testthat/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (testthat) * installing *source* package ‘IRanges’ ... ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c CompressedList_class.c -o CompressedList_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c Grouping_class.c -o Grouping_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c IRanges_class.c -o IRanges_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c IRanges_constructor.c -o IRanges_constructor.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c NCList.c -o NCList.o NCList.c:1173:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function] 1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist, | ^~~~~~~~~~~~~~~~~~~~~~~~~ NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function] 202 | static const NCList *next_top_down(const NCList *nclist) | ^~~~~~~~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c R_init_IRanges.c -o R_init_IRanges.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c Ranges_class.c -o Ranges_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c RleViews_utils.c -o RleViews_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c coverage_methods.c -o coverage_methods.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c extractListFragments.c -o extractListFragments.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c inter_range_methods.c -o inter_range_methods.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-IRanges/00new/IRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IRanges) * installing *source* package ‘fgsea’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/BH/include' -I/usr/local/include -fpic -Wall -pedantic -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/BH/include' -I/usr/local/include -fpic -Wall -pedantic -c esCalculation.cpp -o esCalculation.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/BH/include' -I/usr/local/include -fpic -Wall -pedantic -c fastGSEA.cpp -o fastGSEA.o fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)’: fastGSEA.cpp:446:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 446 | for (int j = 0; j < S.size(); ++j) { | ~~^~~~~~~~~~ g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/BH/include' -I/usr/local/include -fpic -Wall -pedantic -c fgseaMultilevel.cpp -o fgseaMultilevel.o In file included from /opt/R-rc/lib/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/arg.hpp:25, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /opt/R-rc/lib/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /opt/R-rc/lib/R/library/BH/include/boost/lexical_cast.hpp:30, from /opt/R-rc/lib/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12, from /opt/R-rc/lib/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14, from /opt/R-rc/lib/R/library/BH/include/boost/math/constants/constants.hpp:14, from /opt/R-rc/lib/R/library/BH/include/boost/math/special_functions/digamma.hpp:20, from fgseaMultilevelSupplement.h:9, from fgseaMultilevel.cpp:2: /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ fgseaMultilevel.cpp: In function ‘Rcpp::DataFrame fgseaMultilevelCpp(const NumericVector&, const NumericVector&, int, int, int, double, bool)’: fgseaMultilevel.cpp:10:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10 | for (int i = 0; i < posRanks.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/BH/include' -I/usr/local/include -fpic -Wall -pedantic -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o In file included from /opt/R-rc/lib/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/arg.hpp:25, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /opt/R-rc/lib/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /opt/R-rc/lib/R/library/BH/include/boost/lexical_cast.hpp:30, from /opt/R-rc/lib/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12, from /opt/R-rc/lib/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14, from /opt/R-rc/lib/R/library/BH/include/boost/math/constants/constants.hpp:14, from /opt/R-rc/lib/R/library/BH/include/boost/math/special_functions/digamma.hpp:20, from fgseaMultilevelSupplement.h:9, from fgseaMultilevelSupplement.cpp:1: /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::duplicateSamples()’: fgseaMultilevelSupplement.cpp:44:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 44 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) { | ~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:54:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 54 | for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) { | ~~~~~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:63:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 63 | for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::extend(double, int, double)’: fgseaMultilevelSupplement.cpp:77:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 77 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) { | ~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:81:16: warning: unused variable ‘currentES’ [-Wunused-variable] 81 | double currentES = calcES(ranks, currentSamples[sampleId]); | ^~~~~~~~~ fgseaMultilevelSupplement.cpp:94:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 94 | for (int j = 0; j < sampleSize; ++j) { | ~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:101:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 101 | for (int i = 0; i < sampleSize; ++i) { | ~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:116:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 116 | for (int moves = 0; moves < sampleSize * pathwaySize;) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:117:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 117 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) { | ~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:122:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 122 | for (int i = 0; i < sampleSize; ++i) { | ~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp: In member function ‘int EsRuler::perturbate(const std::vector&, int, EsRuler::SampleChunks&, double, std::mt19937&)’: fgseaMultilevelSupplement.cpp:264:14: warning: unused variable ‘fl’ [-Wunused-variable] 264 | bool fl = false; | ^~ g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/BH/include' -I/usr/local/include -fpic -Wall -pedantic -c util.cpp -o util.o g++ -std=gnu++11 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o fgsea.so RcppExports.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o util.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-fgsea/00new/fgsea/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fgsea) * installing *source* package ‘viper’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (viper) * installing *source* package ‘bcellViper’ ... ** using staged installation ** data ** inst ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bcellViper) * installing *source* package ‘GenomeInfoDb’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomeInfoDb) * installing *source* package ‘XVector’ ... ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c: In function ‘RDS_extract_subarray’: RDS_random_access.c:796:18: warning: unused variable ‘ans’ [-Wunused-variable] 796 | SEXP subscript, ans; | ^~~ RDS_random_access.c:793:11: warning: variable ‘x_type’ set but not used [-Wunused-but-set-variable] 793 | SEXPTYPE x_type; | ^~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c R_init_XVector.c -o R_init_XVector.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c SharedDouble_class.c -o SharedDouble_class.o SharedDouble_class.c: In function ‘SharedDouble_get_show_string’: SharedDouble_class.c:42:68: warning: format ‘%p’ expects argument of type ‘void *’, but argument 5 has type ‘double *’ [-Wformat=] 42 | "%d-number SharedDouble object (data starting at memory address %p)", | ~^ | | | void * 43 | tag_length, REAL(tag)); | ~~~~~~~~~ | | | double * gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c SharedInteger_class.c -o SharedInteger_class.o SharedInteger_class.c: In function ‘SharedInteger_get_show_string’: SharedInteger_class.c:41:70: warning: format ‘%p’ expects argument of type ‘void *’, but argument 5 has type ‘int *’ [-Wformat=] 41 | "%d-integer SharedInteger object (data starting at memory address %p)", | ~^ | | | void * | %ls 42 | tag_length, INTEGER(tag)); | ~~~~~~~~~~~~ | | | int * gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c SharedRaw_class.c -o SharedRaw_class.o SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’: SharedRaw_class.c:396:13: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable] 396 | SEXP dest, src_tag; | ^~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c SharedVector_class.c -o SharedVector_class.o SharedVector_class.c: In function ‘address_as_CHARSXP’: SharedVector_class.c:22:31: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=] 22 | snprintf(buf, sizeof(buf), "%p", x); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XDouble_class.c -o XDouble_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XInteger_class.c -o XInteger_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XRawList_comparison.c -o XRawList_comparison.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XRaw_class.c -o XRaw_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XVectorList_class.c -o XVectorList_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XVector_class.c -o XVector_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c io_utils.c -o io_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c slice_methods.c -o slice_methods.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c vector_copy.c -o vector_copy.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c view_summarization_methods.c -o view_summarization_methods.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-XVector/00new/XVector/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XVector) * installing *source* package ‘piano’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (piano) * installing *source* package ‘Biostrings’ ... ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c BAB_class.c -o BAB_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c BitMatrix.c -o BitMatrix.o BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function] 299 | static void BitMatrix_print(BitMatrix *bitmat) | ^~~~~~~~~~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c MIndex_class.c -o MIndex_class.o MIndex_class.c: In function ‘SparseMIndex_endIndex’: MIndex_class.c:184:20: warning: unused variable ‘poffsets_order’ [-Wunused-variable] 184 | IntAE *poffsets, *poffsets_order; | ^~~~~~~~~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c SparseList_utils.c -o SparseList_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XStringSet_class.c -o XStringSet_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XString_class.c -o XString_class.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c XVector_stubs.c -o XVector_stubs.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c align_needwunsQS.c -o align_needwunsQS.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c align_utils.c -o align_utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c find_palindromes.c -o find_palindromes.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c gtestsim.c -o gtestsim.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c inject_code.c -o inject_code.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c letter_frequency.c -o letter_frequency.o letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’: letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable] 957 | int x_width, y_width, x_length, *ans_mat, i, x_pos; | ^~~~~ letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable] 956 | SEXP ans, ans_dimnames; | ^~~~~~~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_PWM.c -o match_PWM.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_pattern.c -o match_pattern.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_pattern_indels.c -o match_pattern_indels.o match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function] 7 | static void test_match_pattern_indels(const char *p, const char *s, | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_pdict.c -o match_pdict.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o match_pdict_ACtree2.c: In function ‘split_and_move_pointers’: match_pdict_ACtree2.c:1031:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1031 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: In function ‘merge_pointers’: match_pdict_ACtree2.c:1076:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1076 | ACnode *node0, *node1, *node2; | ^~~~~ At top level: match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function] 602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function] 139 | static void debug_node_counting_functions(int maxdepth) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_pdict_utils.c -o match_pdict_utils.o match_pdict_utils.c: In function ‘match_ppheadtail0’: match_pdict_utils.c:653:49: warning: unused variable ‘ncol’ [-Wunused-variable] 653 | int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol; | ^~~~ match_pdict_utils.c: In function ‘match_ppheadtail’: match_pdict_utils.c:713:6: warning: unused variable ‘nelt’ [-Wunused-variable] 713 | int nelt, nkey0, nkey1, nkey2, i, key; | ^~~~ match_pdict_utils.c: In function ‘_match_pdict_all_flanks’: match_pdict_utils.c:820:44: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:820:27: warning: unused variable ‘total_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:819:33: warning: unused variable ‘NFC’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~ match_pdict_utils.c:819:26: warning: unused variable ‘nloci’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~~ match_pdict_utils.c:819:20: warning: unused variable ‘ndup’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~ At top level: match_pdict_utils.c:820:27: warning: ‘total_NFC’ defined but not used [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:820:44: warning: ‘subtotal_NFC’ defined but not used [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:261:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function] 261 | static void match_headtail_by_loc(const HeadTail *headtail, | ^~~~~~~~~~~~~~~~~~~~~ gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c match_reporting.c -o match_reporting.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c matchprobes.c -o matchprobes.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c pmatchPattern.c -o pmatchPattern.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c read_fasta_files.c -o read_fasta_files.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c read_fastq_files.c -o read_fastq_files.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c replaceAt.c -o replaceAt.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c replace_letter_at.c -o replace_letter_at.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c strutils.c -o strutils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c translate.c -o translate.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c utils.c -o utils.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/S4Vectors/include' -I'/home/omnipath/local/R/IRanges/include' -I'/home/omnipath/local/R/XVector/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c xscat.c -o xscat.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-Biostrings/00new/Biostrings/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet” Creating a new generic function for ‘strsplit’ in package ‘Biostrings’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’ Creating a new generic function for ‘pattern’ in package ‘Biostrings’ Creating a new generic function for ‘offset’ in package ‘Biostrings’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Biostrings) * installing *source* package ‘KEGGREST’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (KEGGREST) * installing *source* package ‘AnnotationDbi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationDbi) * installing *source* package ‘annotate’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (annotate) * installing *source* package ‘GSEABase’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GSEABase) The downloaded source packages are in ‘/tmp/RtmptI43Pm/downloaded_packages’ Downloading GitHub repo saezlab/CARNIVAL@HEAD cli (3.2.0 -> 3.3.0) [CRAN] tibble (3.1.6 -> 3.1.7) [CRAN] knitr (1.38 -> 1.39 ) [CRAN] dplyr (1.0.8 -> 1.0.9) [CRAN] rmarkdown (2.13 -> 2.14 ) [CRAN] Installing 5 packages: cli, tibble, knitr, dplyr, rmarkdown trying URL 'https://cloud.r-project.org/src/contrib/cli_3.3.0.tar.gz' Content type 'application/x-gzip' length 495823 bytes (484 KB) ================================================== downloaded 484 KB trying URL 'https://cloud.r-project.org/src/contrib/tibble_3.1.7.tar.gz' Content type 'application/x-gzip' length 674873 bytes (659 KB) ================================================== downloaded 659 KB trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.39.tar.gz' Content type 'application/x-gzip' length 898418 bytes (877 KB) ================================================== downloaded 877 KB trying URL 'https://cloud.r-project.org/src/contrib/dplyr_1.0.9.tar.gz' Content type 'application/x-gzip' length 957637 bytes (935 KB) ================================================== downloaded 935 KB trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.14.tar.gz' Content type 'application/x-gzip' length 3241807 bytes (3.1 MB) ================================================== downloaded 3.1 MB * installing *source* package ‘cli’ ... ** package ‘cli’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c ansi.c -o ansi.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c cleancall.c -o cleancall.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c diff.c -o diff.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c errors.c -o errors.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c md5.c -o md5.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress-altrep.c -o progress-altrep.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress.c -o progress.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c sha256.c -o sha256.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c thread.c -o thread.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c tty.c -o tty.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c utf8.c -o utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c win-utf8.c -o win-utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c winfiles.c -o winfiles.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o init.o md5.o progress-altrep.o progress.o sha256.o thread.o tty.o utf8.o win-utf8.o winfiles.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-cli/00new/cli/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cli) * installing *source* package ‘tibble’ ... ** package ‘tibble’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c attributes.c -o attributes.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c coerce.c -o coerce.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c matrixToDataFrame.c -o matrixToDataFrame.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o tibble.so attributes.o coerce.o init.o matrixToDataFrame.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-tibble/00new/tibble/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tibble) * installing *source* package ‘knitr’ ... ** package ‘knitr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (knitr) * installing *source* package ‘dplyr’ ... ** package ‘dplyr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c chop.cpp -o chop.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c filter.cpp -o filter.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c funs.cpp -o funs.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c group_by.cpp -o group_by.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c group_data.cpp -o group_data.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c imports.cpp -o imports.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c init.cpp -o init.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c mask.cpp -o mask.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c mutate.cpp -o mutate.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c slice.cpp -o slice.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -Wall -pedantic -c summarise.cpp -o summarise.o g++ -std=gnu++14 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-dplyr/00new/dplyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dplyr) * installing *source* package ‘rmarkdown’ ... ** package ‘rmarkdown’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rmarkdown) The downloaded source packages are in ‘/tmp/RtmptI43Pm/downloaded_packages’ * checking for file ‘/tmp/RtmptI43Pm/remotesdf6b14470f90d/saezlab-CARNIVAL-8b3f0df/DESCRIPTION’ ... OK * preparing ‘CARNIVAL’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Omitted ‘LazyData’ from DESCRIPTION * building ‘CARNIVAL_2.5.1.tar.gz’ * installing *source* package ‘CARNIVAL’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CARNIVAL) [ Finished: 2022-05-04 12:12:11 ]