CRAN Package Check Results for Package BioUtils

Last updated on 2026-08-03 23:50:27 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.1.3	2.47	125.87	128.34	OK
r-devel-linux-x86_64-debian-gcc	0.1.3	1.85	99.25	101.10	NOTE
r-devel-linux-x86_64-fedora-clang	0.1.3			200.07	OK
r-devel-linux-x86_64-fedora-gcc	0.1.3			94.26	OK
r-devel-windows-x86_64	0.1.3	6.00	192.00	198.00	OK
r-patched-linux-x86_64	0.1.3	3.02	91.42	94.44	ERROR
r-release-linux-x86_64	0.1.3	2.37	60.29	62.66	ERROR
r-release-macos-arm64	0.1.3	1.00	82.00	83.00	OK
r-release-macos-x86_64	0.1.3	2.00	223.00	225.00	OK
r-release-windows-x86_64	0.1.3	7.00	82.00	89.00	ERROR
r-oldrel-macos-arm64	0.1.3	1.00	84.00	85.00	OK
r-oldrel-macos-x86_64	0.1.3	2.00	157.00	159.00	OK
r-oldrel-windows-x86_64	0.1.3	8.00	273.00	281.00	OK

Additional issues

donttest

Check Details

Version: 0.1.3
Check: for new files in some other directories
Result: NOTE Found the following files/directories: ‘~/tmp/scratch/Rtmp00KFYm’ ‘~/tmp/scratch/Rtmp03FZLh’ ‘~/tmp/scratch/Rtmp04rdh6’ ‘~/tmp/scratch/Rtmp08a3ia’ ‘~/tmp/scratch/Rtmp0SgILW’ ‘~/tmp/scratch/Rtmp0vleX8’ ‘~/tmp/scratch/Rtmp0zmG5y’ ‘~/tmp/scratch/Rtmp1ee5et’ ‘~/tmp/scratch/Rtmp23vvTR’ ‘~/tmp/scratch/Rtmp36FNWi’ ‘~/tmp/scratch/Rtmp3DBhv8’ ‘~/tmp/scratch/Rtmp3DKopT’ ‘~/tmp/scratch/Rtmp3NJE2K’ ‘~/tmp/scratch/Rtmp4y0NuY’ ‘~/tmp/scratch/Rtmp5EA3Jb’ ‘~/tmp/scratch/Rtmp5Y2EW5’ ‘~/tmp/scratch/Rtmp66zV3f’ ‘~/tmp/scratch/Rtmp68mbMA’ ‘~/tmp/scratch/Rtmp6K95Io’ ‘~/tmp/scratch/Rtmp6VFfha’ ‘~/tmp/scratch/Rtmp6aIdDB’ ‘~/tmp/scratch/Rtmp6eEVOq’ ‘~/tmp/scratch/Rtmp7EkKlT’ ‘~/tmp/scratch/Rtmp7kirAC’ ‘~/tmp/scratch/Rtmp82ElQE’ ‘~/tmp/scratch/Rtmp8KFmW6’ ‘~/tmp/scratch/Rtmp8ws5o0’ ‘~/tmp/scratch/Rtmp9fGjCW’ ‘~/tmp/scratch/RtmpA3eixj’ ‘~/tmp/scratch/RtmpAZEhqD’ ‘~/tmp/scratch/RtmpAZvdo3’ ‘~/tmp/scratch/RtmpBsn94A’ ‘~/tmp/scratch/RtmpD4tt9R’ ‘~/tmp/scratch/RtmpDHy5l6’ ‘~/tmp/scratch/RtmpE7RHdg’ ‘~/tmp/scratch/RtmpEeqPFo’ ‘~/tmp/scratch/RtmpH2sgfI’ ‘~/tmp/scratch/RtmpHCtPS0’ ‘~/tmp/scratch/RtmpHqqv7S’ ‘~/tmp/scratch/RtmpI6BxFz’ ‘~/tmp/scratch/RtmpITzCim’ ‘~/tmp/scratch/RtmpIcmMW7’ ‘~/tmp/scratch/RtmpIsVq3i’ ‘~/tmp/scratch/RtmpKchlYi’ ‘~/tmp/scratch/RtmpKer2u8’ ‘~/tmp/scratch/RtmpLYUSEe’ ‘~/tmp/scratch/RtmpLcEdiu’ ‘~/tmp/scratch/RtmpLnzZbj’ ‘~/tmp/scratch/RtmpLskRE9’ ‘~/tmp/scratch/RtmpMm30gA’ ‘~/tmp/scratch/RtmpN7wFKg’ ‘~/tmp/scratch/RtmpNNjw4C’ ‘~/tmp/scratch/RtmpNYyufE’ ‘~/tmp/scratch/RtmpNtj57e’ ‘~/tmp/scratch/RtmpNvKuqi’ ‘~/tmp/scratch/RtmpO3mE49’ ‘~/tmp/scratch/RtmpOC167g’ ‘~/tmp/scratch/RtmpOFQuQ5’ ‘~/tmp/scratch/RtmpONcZU5’ ‘~/tmp/scratch/RtmpOS1vwg’ ‘~/tmp/scratch/RtmpP7CkEl’ ‘~/tmp/scratch/RtmpPkCXFw’ ‘~/tmp/scratch/RtmpPsSCx9’ ‘~/tmp/scratch/RtmpQdbORi’ ‘~/tmp/scratch/RtmpT1h0jT’ ‘~/tmp/scratch/RtmpTBoTUz’ ‘~/tmp/scratch/RtmpTFcTzh’ ‘~/tmp/scratch/RtmpTtOh26’ ‘~/tmp/scratch/RtmpTv3w1a’ ‘~/tmp/scratch/RtmpUNN5M3’ ‘~/tmp/scratch/RtmpUe1XIr’ ‘~/tmp/scratch/RtmpV2To7c’ ‘~/tmp/scratch/RtmpV3usxg’ ‘~/tmp/scratch/RtmpV444NZ’ ‘~/tmp/scratch/RtmpWVQofF’ ‘~/tmp/scratch/RtmpWiR5Uq’ ‘~/tmp/scratch/RtmpWvqa40’ ‘~/tmp/scratch/RtmpXFiypk’ ‘~/tmp/scratch/RtmpYDriQz’ ‘~/tmp/scratch/RtmpaD9oAp’ ‘~/tmp/scratch/RtmpaL72IE’ ‘~/tmp/scratch/Rtmpai1uyG’ ‘~/tmp/scratch/Rtmpb4SWEl’ ‘~/tmp/scratch/RtmpcTlhip’ ‘~/tmp/scratch/RtmpcdAZwB’ ‘~/tmp/scratch/RtmpchujXw’ ‘~/tmp/scratch/Rtmpd0eZDb’ ‘~/tmp/scratch/Rtmpd39GTu’ ‘~/tmp/scratch/RtmpdDNWSo’ ‘~/tmp/scratch/RtmpdOPlvY’ ‘~/tmp/scratch/RtmpdSZlJ3’ ‘~/tmp/scratch/RtmpduSBnp’ ‘~/tmp/scratch/RtmpeHPgIC’ ‘~/tmp/scratch/RtmpeKYNFT’ ‘~/tmp/scratch/RtmpeZadxU’ ‘~/tmp/scratch/RtmpeaEE2S’ ‘~/tmp/scratch/RtmpfwmpB0’ ‘~/tmp/scratch/RtmpgSvPpN’ ‘~/tmp/scratch/Rtmph7K0th’ ‘~/tmp/scratch/RtmphUV8sl’ ‘~/tmp/scratch/Rtmpi7qwbA’ ‘~/tmp/scratch/RtmpihIVqX’ ‘~/tmp/scratch/Rtmpj7Hshr’ ‘~/tmp/scratch/RtmpjJEOkd’ ‘~/tmp/scratch/RtmpjnK1ZE’ ‘~/tmp/scratch/Rtmpjxscsk’ ‘~/tmp/scratch/RtmpkJ17kP’ ‘~/tmp/scratch/RtmpkvKOUN’ ‘~/tmp/scratch/Rtmpl6FxI4’ ‘~/tmp/scratch/RtmpmJzHwJ’ ‘~/tmp/scratch/RtmpmxKEQc’ ‘~/tmp/scratch/RtmpnjEi3m’ ‘~/tmp/scratch/Rtmpnrw6mU’ ‘~/tmp/scratch/RtmpobGqa3’ ‘~/tmp/scratch/RtmppPHds1’ ‘~/tmp/scratch/Rtmppmyk5B’ ‘~/tmp/scratch/Rtmpq9R8v0’ ‘~/tmp/scratch/Rtmpqa7Yar’ ‘~/tmp/scratch/RtmpqqXo5J’ ‘~/tmp/scratch/Rtmpr6v0Bu’ ‘~/tmp/scratch/RtmprajhDT’ ‘~/tmp/scratch/Rtmps3wejy’ ‘~/tmp/scratch/RtmpsLajKQ’ ‘~/tmp/scratch/Rtmpse9mck’ ‘~/tmp/scratch/RtmptSRO5L’ ‘~/tmp/scratch/RtmptaAug0’ ‘~/tmp/scratch/RtmptdnX4h’ ‘~/tmp/scratch/Rtmpu3qVhC’ ‘~/tmp/scratch/RtmpuFOc5q’ ‘~/tmp/scratch/RtmpulH10Y’ ‘~/tmp/scratch/RtmpumPsXt’ ‘~/tmp/scratch/Rtmpumx4V7’ ‘~/tmp/scratch/RtmpvR6Kfg’ ‘~/tmp/scratch/RtmpwfnQ80’ ‘~/tmp/scratch/Rtmpwvk0Mn’ ‘~/tmp/scratch/RtmpwvumEQ’ ‘~/tmp/scratch/RtmpxsWcJs’ ‘~/tmp/scratch/RtmpxuFwQB’ ‘~/tmp/scratch/RtmpxvoZ0f’ ‘~/tmp/scratch/RtmpyeK8kL’ ‘~/tmp/scratch/RtmpzcOYjJ’ ‘~/tmp/scratch/RtmpzdeIJt’ ‘~/tmp/scratch/RtmpzsphGF’ ‘~/tmp/scratch/ccDlyoRF.s’ ‘~/tmp/scratch/quarto-sessione48a53feec0e950d’ ‘~/tmp/scratch/xvfb-run.0c5ZYB’ ‘~/tmp/scratch/xvfb-run.2BLZk8’ ‘~/tmp/scratch/xvfb-run.2aVkKe’ ‘~/tmp/scratch/xvfb-run.3EHB0O’ ‘~/tmp/scratch/xvfb-run.3FFG1L’ ‘~/tmp/scratch/xvfb-run.4PFFmC’ ‘~/tmp/scratch/xvfb-run.5D2XvI’ ‘~/tmp/scratch/xvfb-run.6hTk0U’ ‘~/tmp/scratch/xvfb-run.7BM5dV’ ‘~/tmp/scratch/xvfb-run.9h13qm’ ‘~/tmp/scratch/xvfb-run.ALbGw9’ ‘~/tmp/scratch/xvfb-run.B1Ryl3’ ‘~/tmp/scratch/xvfb-run.Bewcgj’ ‘~/tmp/scratch/xvfb-run.BgfzW3’ ‘~/tmp/scratch/xvfb-run.C1lmlc’ ‘~/tmp/scratch/xvfb-run.C2DmJH’ ‘~/tmp/scratch/xvfb-run.CRTlOe’ ‘~/tmp/scratch/xvfb-run.DxquDk’ ‘~/tmp/scratch/xvfb-run.EzMnVS’ ‘~/tmp/scratch/xvfb-run.GuwkMF’ ‘~/tmp/scratch/xvfb-run.HVZ6ME’ ‘~/tmp/scratch/xvfb-run.HkactV’ ‘~/tmp/scratch/xvfb-run.IPuUgD’ ‘~/tmp/scratch/xvfb-run.LzuSm8’ ‘~/tmp/scratch/xvfb-run.MHUP3c’ ‘~/tmp/scratch/xvfb-run.NORnPQ’ ‘~/tmp/scratch/xvfb-run.QRICOB’ ‘~/tmp/scratch/xvfb-run.RZGSSq’ ‘~/tmp/scratch/xvfb-run.RuXxiU’ ‘~/tmp/scratch/xvfb-run.SmRg5u’ ‘~/tmp/scratch/xvfb-run.TGkkxC’ ‘~/tmp/scratch/xvfb-run.Tryfxy’ ‘~/tmp/scratch/xvfb-run.UW4AaN’ ‘~/tmp/scratch/xvfb-run.YT9Wfz’ ‘~/tmp/scratch/xvfb-run.ZU5dce’ ‘~/tmp/scratch/xvfb-run.btFcqJ’ ‘~/tmp/scratch/xvfb-run.cG45AU’ ‘~/tmp/scratch/xvfb-run.cIIqIb’ ‘~/tmp/scratch/xvfb-run.d9SQSR’ ‘~/tmp/scratch/xvfb-run.dZRSjh’ ‘~/tmp/scratch/xvfb-run.eHVuq2’ ‘~/tmp/scratch/xvfb-run.fTJg54’ ‘~/tmp/scratch/xvfb-run.faM3IA’ ‘~/tmp/scratch/xvfb-run.fnd6So’ ‘~/tmp/scratch/xvfb-run.gMbynU’ ‘~/tmp/scratch/xvfb-run.gQ3zSi’ ‘~/tmp/scratch/xvfb-run.gZxhR3’ ‘~/tmp/scratch/xvfb-run.glucET’ ‘~/tmp/scratch/xvfb-run.hlwLvA’ ‘~/tmp/scratch/xvfb-run.j4ehdE’ ‘~/tmp/scratch/xvfb-run.j50ZLf’ ‘~/tmp/scratch/xvfb-run.nLnKRd’ ‘~/tmp/scratch/xvfb-run.nzyYvU’ ‘~/tmp/scratch/xvfb-run.osxZBG’ ‘~/tmp/scratch/xvfb-run.qdEoBh’ ‘~/tmp/scratch/xvfb-run.tdN2RY’ ‘~/tmp/scratch/xvfb-run.tge1A5’ ‘~/tmp/scratch/xvfb-run.uFERl7’ ‘~/tmp/scratch/xvfb-run.v1BmfX’ ‘~/tmp/scratch/xvfb-run.vEWs7S’ ‘~/tmp/scratch/xvfb-run.vKUAKA’ ‘~/tmp/scratch/xvfb-run.vZl05v’ ‘~/tmp/scratch/xvfb-run.wNL27I’ ‘~/tmp/scratch/xvfb-run.yl4uK5’ ‘~/tmp/scratch/xvfb-run.yoTMdM’ Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘bioutils-case-study.Rmd’ using rmarkdown --- finished re-building ‘bioutils-case-study.Rmd’ --- re-building ‘rcc-visual-analytics.Rmd’ using rmarkdown Quitting from rcc-visual-analytics.Rmd:153-162 [load] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/httr2_failure> Error in `httr2::req_perform()`: ! Failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Transferred a partial file [ftp.ncbi.nlm.nih.gov]: end of response with 1030542 bytes missing --- Backtrace: ▆ 1. ├─BioUtils::extract.expression(...) 2. └─BioUtils::load.geo.soft(accession = "GDS507", log.transform = TRUE) 3. └─GEOquery::getGEO(accession, destdir = tempdir(), GSEMatrix = FALSE) 4. └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL) 5. └─GEOquery:::downloadFile(myurl, destfile, mode) 6. ├─base::tryCatch(...) 7. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. └─httr2::req_perform(req) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rcc-visual-analytics.Rmd' failed with diagnostics: Failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Transferred a partial file [ftp.ncbi.nlm.nih.gov]: end of response with 1030542 bytes missing --- failed re-building ‘rcc-visual-analytics.Rmd’ SUMMARY: processing the following file failed: ‘rcc-visual-analytics.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-patched-linux-x86_64

Version: 0.1.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘bioutils-case-study.Rmd’ using rmarkdown Quitting from bioutils-case-study.Rmd:72-76 [load] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/httr2_http_403> Error in `httr2::req_perform()`: ! HTTP 403 Forbidden. --- Backtrace: ▆ 1. └─BioUtils::load.geo.soft("", "GDS507", log.transform = TRUE) 2. └─GEOquery::getGEO(accession, destdir = tempdir(), GSEMatrix = FALSE) 3. └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL) 4. └─GEOquery:::downloadFile(myurl, destfile, mode) 5. ├─base::tryCatch(...) 6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 9. └─httr2::req_perform(req) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'bioutils-case-study.Rmd' failed with diagnostics: HTTP 403 Forbidden. --- failed re-building ‘bioutils-case-study.Rmd’ --- re-building ‘rcc-visual-analytics.Rmd’ using rmarkdown Quitting from rcc-visual-analytics.Rmd:153-162 [load] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/httr2_http_403> Error in `httr2::req_perform()`: ! HTTP 403 Forbidden. --- Backtrace: ▆ 1. ├─BioUtils::extract.expression(...) 2. └─BioUtils::load.geo.soft(accession = "GDS507", log.transform = TRUE) 3. └─GEOquery::getGEO(accession, destdir = tempdir(), GSEMatrix = FALSE) 4. └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL) 5. └─GEOquery:::downloadFile(myurl, destfile, mode) 6. ├─base::tryCatch(...) 7. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. └─httr2::req_perform(req) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rcc-visual-analytics.Rmd' failed with diagnostics: HTTP 403 Forbidden. --- failed re-building ‘rcc-visual-analytics.Rmd’ SUMMARY: processing the following files failed: ‘bioutils-case-study.Rmd’ ‘rcc-visual-analytics.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64

Version: 0.1.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'bioutils-case-study.Rmd' using rmarkdown Quitting from bioutils-case-study.Rmd:72-76 [load] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/httr2_http_403> Error in `httr2::req_perform()`: ! HTTP 403 Forbidden. --- Backtrace: ▆ 1. └─BioUtils::load.geo.soft("", "GDS507", log.transform = TRUE) 2. └─GEOquery::getGEO(accession, destdir = tempdir(), GSEMatrix = FALSE) 3. └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL) 4. └─GEOquery:::downloadFile(myurl, destfile, mode) 5. ├─base::tryCatch(...) 6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 9. └─httr2::req_perform(req) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'bioutils-case-study.Rmd' failed with diagnostics: HTTP 403 Forbidden. --- failed re-building 'bioutils-case-study.Rmd' --- re-building 'rcc-visual-analytics.Rmd' using rmarkdown Quitting from rcc-visual-analytics.Rmd:153-162 [load] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/httr2_http_403> Error in `httr2::req_perform()`: ! HTTP 403 Forbidden. --- Backtrace: ▆ 1. ├─BioUtils::extract.expression(...) 2. └─BioUtils::load.geo.soft(accession = "GDS507", log.transform = TRUE) 3. └─GEOquery::getGEO(accession, destdir = tempdir(), GSEMatrix = FALSE) 4. └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL) 5. └─GEOquery:::downloadFile(myurl, destfile, mode) 6. ├─base::tryCatch(...) 7. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. └─httr2::req_perform(req) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rcc-visual-analytics.Rmd' failed with diagnostics: HTTP 403 Forbidden. --- failed re-building 'rcc-visual-analytics.Rmd' SUMMARY: processing the following files failed: 'bioutils-case-study.Rmd' 'rcc-visual-analytics.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-release-windows-x86_64