CRAN Package Check Results for Package BioUtils

Last updated on 2026-08-02 13:49:02 CEST.

Flavor	Version	T_install	T_check	T_total	Status
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	1.71	96.50	98.21	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	5.00	202.00	207.00	OK
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	195.00	203.00	ERROR

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/Rtmp0YrCiS’ ‘~/tmp/scratch/Rtmp1D5eXn’ ‘~/tmp/scratch/Rtmp1KxPOO’ ‘~/tmp/scratch/Rtmp26Fk1v’ ‘~/tmp/scratch/Rtmp2WT8Qx’ ‘~/tmp/scratch/Rtmp2kTIlh’ ‘~/tmp/scratch/Rtmp3XyUx0’ ‘~/tmp/scratch/Rtmp3ePjuf’ ‘~/tmp/scratch/Rtmp3kJBu1’ ‘~/tmp/scratch/Rtmp3w9beH’ ‘~/tmp/scratch/Rtmp4607Nf’ ‘~/tmp/scratch/Rtmp4IImEX’ ‘~/tmp/scratch/Rtmp5Dtpjz’ ‘~/tmp/scratch/Rtmp66KVcd’ ‘~/tmp/scratch/Rtmp6B6RhQ’ ‘~/tmp/scratch/Rtmp6bwq55’ ‘~/tmp/scratch/Rtmp6klOKA’ ‘~/tmp/scratch/Rtmp6yYxKn’ ‘~/tmp/scratch/Rtmp7pU2GO’ ‘~/tmp/scratch/Rtmp7xmuCO’ ‘~/tmp/scratch/Rtmp8Puex9’ ‘~/tmp/scratch/Rtmp9ZLwjN’ ‘~/tmp/scratch/Rtmp9qNVnQ’ ‘~/tmp/scratch/Rtmp9woRvA’ ‘~/tmp/scratch/RtmpA8usvY’ ‘~/tmp/scratch/RtmpAP3Vd7’ ‘~/tmp/scratch/RtmpARFSlS’ ‘~/tmp/scratch/RtmpBGE76W’ ‘~/tmp/scratch/RtmpBKgwl5’ ‘~/tmp/scratch/RtmpC7dNqU’ ‘~/tmp/scratch/RtmpCrSdQT’ ‘~/tmp/scratch/RtmpDP5eE7’ ‘~/tmp/scratch/RtmpEUSHRW’ ‘~/tmp/scratch/RtmpEdVdvh’ ‘~/tmp/scratch/RtmpEggTlU’ ‘~/tmp/scratch/RtmpF2MOIs’ ‘~/tmp/scratch/RtmpFk9C8d’ ‘~/tmp/scratch/RtmpG3YCPb’ ‘~/tmp/scratch/RtmpGow7kZ’ ‘~/tmp/scratch/RtmpHJxakK’ ‘~/tmp/scratch/RtmpHYwnob’ ‘~/tmp/scratch/RtmpIAypuj’ ‘~/tmp/scratch/RtmpJQYeIU’ ‘~/tmp/scratch/RtmpJb1k5O’ ‘~/tmp/scratch/RtmpJnqBRt’ ‘~/tmp/scratch/RtmpJt0Xzx’ ‘~/tmp/scratch/RtmpKYOO8o’ ‘~/tmp/scratch/RtmpKfEFVU’ ‘~/tmp/scratch/RtmpKjZpIs’ ‘~/tmp/scratch/RtmpKziv1F’ ‘~/tmp/scratch/RtmpL0ZXLJ’ ‘~/tmp/scratch/RtmpL26Tot’ ‘~/tmp/scratch/RtmpLVMFtM’ ‘~/tmp/scratch/RtmpLXMOHb’ ‘~/tmp/scratch/RtmpLwVuoq’ ‘~/tmp/scratch/RtmpMChZDb’ ‘~/tmp/scratch/RtmpMF3CYE’ ‘~/tmp/scratch/RtmpMo5hTH’ ‘~/tmp/scratch/RtmpNhlgjX’ ‘~/tmp/scratch/RtmpOs9MZh’ ‘~/tmp/scratch/RtmpPOfpX1’ ‘~/tmp/scratch/RtmpPt5WuT’ ‘~/tmp/scratch/RtmpPtut3m’ ‘~/tmp/scratch/RtmpPxTnS5’ ‘~/tmp/scratch/RtmpQBtbMK’ ‘~/tmp/scratch/RtmpQNsg6P’ ‘~/tmp/scratch/RtmpQSaaAM’ ‘~/tmp/scratch/RtmpQlHLkb’ ‘~/tmp/scratch/RtmpQzdIPq’ ‘~/tmp/scratch/RtmpR9cRiq’ ‘~/tmp/scratch/RtmpRKG2ci’ ‘~/tmp/scratch/RtmpRdJiqD’ ‘~/tmp/scratch/RtmpRj211d’ ‘~/tmp/scratch/RtmpSO4mEG’ ‘~/tmp/scratch/RtmpSfTkPu’ ‘~/tmp/scratch/RtmpSiQabf’ ‘~/tmp/scratch/RtmpTCVJwg’ ‘~/tmp/scratch/RtmpTuITHv’ ‘~/tmp/scratch/RtmpUtWPJA’ ‘~/tmp/scratch/RtmpUwkUJR’ ‘~/tmp/scratch/RtmpV28S1h’ ‘~/tmp/scratch/RtmpV9odxD’ ‘~/tmp/scratch/RtmpVi0JvT’ ‘~/tmp/scratch/RtmpVl2u3t’ ‘~/tmp/scratch/RtmpW7Iv11’ ‘~/tmp/scratch/RtmpWq1HUp’ ‘~/tmp/scratch/RtmpXfkGui’ ‘~/tmp/scratch/RtmpXhCtnf’ ‘~/tmp/scratch/RtmpYUM13d’ ‘~/tmp/scratch/RtmpYXcDy5’ ‘~/tmp/scratch/RtmpYYLc1p’ ‘~/tmp/scratch/RtmpZFRfcg’ ‘~/tmp/scratch/RtmpZj5IG7’ ‘~/tmp/scratch/Rtmpa8iWfK’ ‘~/tmp/scratch/RtmpaIpAYL’ ‘~/tmp/scratch/RtmpaMG7zq’ ‘~/tmp/scratch/RtmpbVbdyp’ ‘~/tmp/scratch/RtmpcDbvZi’ ‘~/tmp/scratch/Rtmpcg14vX’ ‘~/tmp/scratch/RtmpcmNZNT’ ‘~/tmp/scratch/Rtmpdd241Y’ ‘~/tmp/scratch/RtmpdkL5GE’ ‘~/tmp/scratch/RtmpeosX2Y’ ‘~/tmp/scratch/RtmpeuME9e’ ‘~/tmp/scratch/RtmpfmLRe7’ ‘~/tmp/scratch/Rtmpfo7ImX’ ‘~/tmp/scratch/Rtmpfuszg3’ ‘~/tmp/scratch/Rtmpg6dvLZ’ ‘~/tmp/scratch/RtmpgJuwqx’ ‘~/tmp/scratch/Rtmpgg0LrJ’ ‘~/tmp/scratch/RtmphP7S8y’ ‘~/tmp/scratch/RtmphoTsjm’ ‘~/tmp/scratch/RtmpiBgn5D’ ‘~/tmp/scratch/RtmpiZfVkI’ ‘~/tmp/scratch/RtmpjXAkYx’ ‘~/tmp/scratch/RtmpjXeucC’ ‘~/tmp/scratch/RtmpjxCTJw’ ‘~/tmp/scratch/RtmpkD700d’ ‘~/tmp/scratch/RtmpkJWrY7’ ‘~/tmp/scratch/RtmpkJbCJX’ ‘~/tmp/scratch/RtmpkixMiv’ ‘~/tmp/scratch/Rtmpl7ax0u’ ‘~/tmp/scratch/RtmplVcVLS’ ‘~/tmp/scratch/RtmpmRZlkz’ ‘~/tmp/scratch/Rtmpn2Ut0D’ ‘~/tmp/scratch/RtmpnM4qyo’ ‘~/tmp/scratch/RtmpnnTpxJ’ ‘~/tmp/scratch/RtmpoBaUrp’ ‘~/tmp/scratch/RtmppI6iuI’ ‘~/tmp/scratch/RtmpqdTS9V’ ‘~/tmp/scratch/RtmprMB6UL’ ‘~/tmp/scratch/RtmprQ3DSP’ ‘~/tmp/scratch/RtmpsLDCiM’ ‘~/tmp/scratch/RtmpsSpkgj’ ‘~/tmp/scratch/Rtmpuf09tM’ ‘~/tmp/scratch/Rtmpv3Ekia’ ‘~/tmp/scratch/RtmpvDcDHU’ ‘~/tmp/scratch/RtmpvF7PJm’ ‘~/tmp/scratch/Rtmpvn3ipQ’ ‘~/tmp/scratch/Rtmpw6RJr7’ ‘~/tmp/scratch/RtmpwGeeKF’ ‘~/tmp/scratch/RtmpwIdCOA’ ‘~/tmp/scratch/RtmpwL76n2’ ‘~/tmp/scratch/RtmpwRwhF6’ ‘~/tmp/scratch/RtmpxPit3v’ ‘~/tmp/scratch/RtmpxVHQhL’ ‘~/tmp/scratch/RtmpxWpn9r’ ‘~/tmp/scratch/RtmpxfV7iS’ ‘~/tmp/scratch/Rtmpxmn9fu’ ‘~/tmp/scratch/RtmpyCGSJZ’ ‘~/tmp/scratch/RtmpycVFxW’ ‘~/tmp/scratch/RtmpzF0CWo’ ‘~/tmp/scratch/ccPv66T8.s’ ‘~/tmp/scratch/xvfb-run.18SkLl’ ‘~/tmp/scratch/xvfb-run.1l1KoW’ ‘~/tmp/scratch/xvfb-run.3tYJzm’ ‘~/tmp/scratch/xvfb-run.5Ks5Vr’ ‘~/tmp/scratch/xvfb-run.69yFAj’ ‘~/tmp/scratch/xvfb-run.6MdAF3’ ‘~/tmp/scratch/xvfb-run.8IycZ1’ ‘~/tmp/scratch/xvfb-run.AzPuSI’ ‘~/tmp/scratch/xvfb-run.C6ZGFE’ ‘~/tmp/scratch/xvfb-run.FIC62A’ ‘~/tmp/scratch/xvfb-run.FNG1oN’ ‘~/tmp/scratch/xvfb-run.H5Mwmo’ ‘~/tmp/scratch/xvfb-run.I0mRHu’ ‘~/tmp/scratch/xvfb-run.LehQsf’ ‘~/tmp/scratch/xvfb-run.LrRHfF’ ‘~/tmp/scratch/xvfb-run.MRm7aS’ ‘~/tmp/scratch/xvfb-run.Mzaz2N’ ‘~/tmp/scratch/xvfb-run.NDQtAz’ ‘~/tmp/scratch/xvfb-run.NlBscP’ ‘~/tmp/scratch/xvfb-run.Otj6GU’ ‘~/tmp/scratch/xvfb-run.Ow088c’ ‘~/tmp/scratch/xvfb-run.Tq71RG’ ‘~/tmp/scratch/xvfb-run.UW5kzM’ ‘~/tmp/scratch/xvfb-run.VNdWDc’ ‘~/tmp/scratch/xvfb-run.VmLndr’ ‘~/tmp/scratch/xvfb-run.WCPBqk’ ‘~/tmp/scratch/xvfb-run.WiE6pU’ ‘~/tmp/scratch/xvfb-run.WpRgQP’ ‘~/tmp/scratch/xvfb-run.XY33TH’ ‘~/tmp/scratch/xvfb-run.YYxpVm’ ‘~/tmp/scratch/xvfb-run.ZCnWvG’ ‘~/tmp/scratch/xvfb-run.ZVvji6’ ‘~/tmp/scratch/xvfb-run.Zjt2YS’ ‘~/tmp/scratch/xvfb-run.bqBTAN’ ‘~/tmp/scratch/xvfb-run.doYiSq’ ‘~/tmp/scratch/xvfb-run.eDFd1K’ ‘~/tmp/scratch/xvfb-run.esBmB0’ ‘~/tmp/scratch/xvfb-run.foA9dC’ ‘~/tmp/scratch/xvfb-run.gD9v5O’ ‘~/tmp/scratch/xvfb-run.gUNeNg’ ‘~/tmp/scratch/xvfb-run.hS3aBI’ ‘~/tmp/scratch/xvfb-run.hdplKh’ ‘~/tmp/scratch/xvfb-run.hi4wWF’ ‘~/tmp/scratch/xvfb-run.huvPao’ ‘~/tmp/scratch/xvfb-run.iaohJ1’ ‘~/tmp/scratch/xvfb-run.l2H3UE’ ‘~/tmp/scratch/xvfb-run.lvJD7N’ ‘~/tmp/scratch/xvfb-run.mjXDBb’ ‘~/tmp/scratch/xvfb-run.mk1vNz’ ‘~/tmp/scratch/xvfb-run.o3ykIH’ ‘~/tmp/scratch/xvfb-run.ois016’ ‘~/tmp/scratch/xvfb-run.pR1a8z’ ‘~/tmp/scratch/xvfb-run.qEgNIV’ ‘~/tmp/scratch/xvfb-run.r5HCDA’ ‘~/tmp/scratch/xvfb-run.sUGj2J’ ‘~/tmp/scratch/xvfb-run.sqiSzh’ ‘~/tmp/scratch/xvfb-run.tpljvL’ ‘~/tmp/scratch/xvfb-run.uQedyO’ ‘~/tmp/scratch/xvfb-run.vpIERP’ ‘~/tmp/scratch/xvfb-run.vzNGxO’ ‘~/tmp/scratch/xvfb-run.wMPhad’ ‘~/tmp/scratch/xvfb-run.wTNUpq’ ‘~/tmp/scratch/xvfb-run.wwnTEq’ ‘~/tmp/scratch/xvfb-run.x6gPNK’ ‘~/tmp/scratch/xvfb-run.xBU4Uo’ ‘~/tmp/scratch/xvfb-run.yvaUED’ 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 Warning: stack imbalance in '<-', 65 then 67 Warning: stack imbalance in 'withVisible', 59 then 61 --- 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 1063310 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 1063310 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-oldrel-windows-x86_64