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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings wppi_1.17.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/wppi.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'wppi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wppi' version '1.17.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... 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
License 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 whether startup messages can be suppressed ... NOTE
[2025-08-15 09:14:05] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 09:14:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:05] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 09:14:05] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-15 09:14:05] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14
[2025-08-15 09:14:05] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:27:25 UTC; windows
[2025-08-15 09:14:05] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-15 09:14:05] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpYdiQa8/fileeb7c750039a4". Did you mean command "update"?
[2025-08-15 09:14:07] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-15 09:14:07] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-15 09:14:08] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-14); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.17.0(2025-08-14); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-15 09:14:08] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:08] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-15 09:14:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:08] [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 ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpOMOVmz/file1e2a445d26513". Did you mean command "update"?
* checking S3 generic/method consistency ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpKE1rk8/filec6143686143f". Did you mean command "update"?
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpC20e9k/file44f060841fc2". Did you mean command "preview"?
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpOYofj0/filea1644d412d1". Did you mean command "update"?
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
[2025-08-15 09:14:37] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 09:14:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:37] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 09:14:37] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-15 09:14:37] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14
[2025-08-15 09:14:37] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:27:25 UTC; windows
[2025-08-15 09:14:37] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-15 09:14:37] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpiMvZyU/fileabb81f10126d". Did you mean command "preview"?
[2025-08-15 09:14:38] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-15 09:14:39] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-15 09:14:39] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-14); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.17.0(2025-08-14); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-15 09:14:39] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:39] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-15 09:14:39] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpgRphuo/file1ff4758e3261". Did you mean command "update"?
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpE37ceE/file1b0ccc555b89". Did you mean command "preview"?
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpQzCu5h/filefbb8787d685a". Did you mean command "update"?
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpiOyxuw/file1ebe02c4e462c". Did you mean command "update"?
* checking Rd \usage sections ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmpsxaxq7/file1850c2f60363e". Did you mean command "update"?
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
wppi                           63.69   1.28   65.07
common_neighbors               49.11   3.21   55.22
score_candidate_genes_from_PPI 36.13   0.93   37.28
random_walk                    33.20   0.86   34.12
prioritization_genes           27.88   0.67   30.70
weighted_adj                   26.11   0.61   26.78
count_genes                    18.89   1.43   18.77
filter_annot_with_network      11.42   0.26   11.71
wppi_data                       8.63   0.19    8.82
subgraph_op                     5.29   0.09    5.40
graph_from_op                   5.06   0.11    5.19
in_omnipath                     5.06   0.04    5.10
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/wppi.Rcheck/00check.log'
for details.