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This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 805/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.41.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025)
git_url: https://git.bioconductor.org/packages/genefu
git_branch: devel
git_last_commit: c144019
git_last_commit_date: 2025-04-15 10:07:38 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for genefu on nebbiolo2

To the developers/maintainers of the genefu package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genefu.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: genefu
Version: 2.41.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings genefu_2.41.0.tar.gz
StartedAt: 2025-08-31 22:57:48 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 23:00:50 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 182.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: genefu.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings genefu_2.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/genefu.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘2.41.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘genefu’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
See ‘/home/biocbuild/bbs-3.22-bioc/meat/genefu.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘AIMS’ ‘biomaRt’ ‘iC10’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘mclust:::grid1’ ‘mclust:::grid2’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) fuzzy.ttest.Rd:41: Lost braces; missing escapes or markup?
    41 | in w1 and w2 should lay in [0,1] and \verb{0 <= (w1[i] + w2[i]) <= 1} for i in {0,1,...,n} where
       |                                                                                ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/genefu.Rcheck/00check.log’
for details.


Installation output

genefu.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL genefu
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘genefu’ ...
** this is package ‘genefu’ version ‘2.41.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** testing if installed package keeps a record of temporary installation path
* DONE (genefu)

Tests output


Example timings

genefu.Rcheck/genefu-Ex.timings

nameusersystemelapsed
bimod0.1990.0070.206
boxplotplus20.0080.0000.007
claudinLow0.5960.0450.641
compareProtoCor1.7850.0851.870
compute.pairw.cor.meta1.5480.0341.582
compute.proto.cor.meta1.2080.0451.253
cordiff.dep0.1180.0000.118
endoPredict0.1170.0010.118
fuzzy.ttest0.1160.0020.118
gene700.2630.0270.290
gene760.1310.0060.137
geneid.map0.1210.0060.127
genius0.2080.0210.229
ggi0.1150.0030.118
ihc40.1020.0030.105
intrinsic.cluster0.3700.0060.364
intrinsic.cluster.predict0.1720.0090.181
map.datasets1.3740.0241.398
molecular.subtyping2.3000.0472.360
npi0.1080.0020.110
oncotypedx0.1570.0030.160
ovcAngiogenic0.1210.0030.124
ovcCrijns0.1170.0020.119
ovcTCGA0.2220.0020.225
ovcYoshihara0.1170.0010.118
pik3cags0.1120.0050.117
power.cor000
ps.cluster0.3480.0090.343
read.m.file0.0190.0000.020
rename.duplicate0.0020.0000.001
rescale0.2300.0060.236
rorS0.1770.0010.179
setcolclass.df0.0020.0000.002
sig.score0.1230.0000.122
spearmanCI0.0010.0000.001
st.gallen0.1040.0030.107
stab.fs0.2120.0000.211
stab.fs.ranking1.3170.0561.373
strescR0.0000.0000.001
subtype.cluster0.6590.0240.684
subtype.cluster.predict0.3030.0060.311
tamr130.1470.0020.149
tbrm000
weighted.meanvar000
write.m.file0.0040.0000.004