[ Started: 2025-02-16 01:39:10 CET ]
[ wppi v1.6.0 for BioC-3.21 from https://github.com/AnaGalhoz37/wppi@main (9b574a4 2022-11-02 08:18:02) ]

* using log directory ‘/mnt/disk0/build/bioc-check/wppi/bioc-3.21/2025-02-16_0137/wppi/wppi.Rcheck’
* using R Under development (unstable) (2025-02-12 r87715)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04 LTS
* using session charset: UTF-8
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wppi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Licence stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:39] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 01:39:39] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-16 00:18:34 UTC; omnipath
[2025-02-16 01:39:39] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-16 01:39:39] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-16 00:18:35 UTC; unix
[2025-02-16 01:39:39] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-16 01:39:39] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-16 01:39:39] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-16 01:39:39] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-16 01:39:39] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:39] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:50] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 01:39:50] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-16 00:18:34 UTC; omnipath
[2025-02-16 01:39:50] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-16 01:39:50] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-16 00:18:35 UTC; unix
[2025-02-16 01:39:50] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-16 01:39:50] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-16 01:39:50] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-16 01:39:50] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-16 01:39:50] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 01:39:50] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/wppi/bioc-3.21/2025-02-16_0137/wppi/wppi.Rcheck/00check.log’
for details.

[ Finished: 2025-02-16 01:43:34 CET ]