Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 809/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genefu 2.40.0 (landing page) Benjamin Haibe-Kains
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. |
Package: genefu |
Version: 2.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genefu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genefu_2.40.0.tar.gz |
StartedAt: 2025-10-14 22:28:07 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 22:30:26 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 139.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: genefu.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genefu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genefu_2.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/genefu.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘genefu/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘genefu’ version ‘2.40.0’ * 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 ‘/Users/biocbuild/bbs-3.21-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 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/genefu.Rcheck/00check.log’ for details.
genefu.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genefu ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘genefu’ ... ** this is package ‘genefu’ version ‘2.40.0’ ** 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)
genefu.Rcheck/genefu-Ex.timings
name | user | system | elapsed | |
bimod | 0.281 | 0.014 | 0.295 | |
boxplotplus2 | 0.008 | 0.001 | 0.009 | |
claudinLow | 0.639 | 0.014 | 0.654 | |
compareProtoCor | 1.368 | 0.030 | 1.404 | |
compute.pairw.cor.meta | 1.800 | 0.030 | 1.839 | |
compute.proto.cor.meta | 1.535 | 0.019 | 1.557 | |
cordiff.dep | 0.167 | 0.006 | 0.172 | |
endoPredict | 0.172 | 0.009 | 0.180 | |
fuzzy.ttest | 0.145 | 0.024 | 0.169 | |
gene70 | 0.353 | 0.019 | 0.372 | |
gene76 | 0.182 | 0.010 | 0.192 | |
geneid.map | 0.155 | 0.010 | 0.166 | |
genius | 0.176 | 0.018 | 0.196 | |
ggi | 0.099 | 0.005 | 0.105 | |
ihc4 | 0.091 | 0.005 | 0.096 | |
intrinsic.cluster | 0.319 | 0.016 | 0.331 | |
intrinsic.cluster.predict | 0.121 | 0.008 | 0.129 | |
map.datasets | 1.402 | 0.026 | 1.431 | |
molecular.subtyping | 2.949 | 0.112 | 3.083 | |
npi | 0.144 | 0.010 | 0.154 | |
oncotypedx | 0.157 | 0.008 | 0.164 | |
ovcAngiogenic | 0.162 | 0.014 | 0.175 | |
ovcCrijns | 0.189 | 0.014 | 0.203 | |
ovcTCGA | 0.239 | 0.009 | 0.249 | |
ovcYoshihara | 0.158 | 0.009 | 0.166 | |
pik3cags | 0.156 | 0.010 | 0.165 | |
power.cor | 0.001 | 0.001 | 0.000 | |
ps.cluster | 0.378 | 0.026 | 0.391 | |
read.m.file | 0.015 | 0.002 | 0.018 | |
rename.duplicate | 0.001 | 0.001 | 0.002 | |
rescale | 0.237 | 0.012 | 0.250 | |
rorS | 0.139 | 0.006 | 0.146 | |
setcolclass.df | 0.001 | 0.000 | 0.001 | |
sig.score | 0.101 | 0.007 | 0.108 | |
spearmanCI | 0 | 0 | 0 | |
st.gallen | 0.097 | 0.004 | 0.101 | |
stab.fs | 0.164 | 0.015 | 0.179 | |
stab.fs.ranking | 1.175 | 0.040 | 1.219 | |
strescR | 0.000 | 0.000 | 0.001 | |
subtype.cluster | 0.553 | 0.042 | 0.600 | |
subtype.cluster.predict | 0.217 | 0.017 | 0.237 | |
tamr13 | 0.110 | 0.008 | 0.119 | |
tbrm | 0 | 0 | 0 | |
weighted.meanvar | 0.000 | 0.000 | 0.001 | |
write.m.file | 0.002 | 0.001 | 0.004 | |