Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-21 11:42 -0400 (Thu, 21 Aug 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" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: genefu |
Version: 2.40.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings genefu_2.40.0.tar.gz |
StartedAt: 2025-08-19 09:20:51 -0000 (Tue, 19 Aug 2025) |
EndedAt: 2025-08-19 09:23:36 -0000 (Tue, 19 Aug 2025) |
EllapsedTime: 165.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: genefu.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings genefu_2.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/genefu.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * 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 ‘/home/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 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 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/genefu.Rcheck/00check.log’ for details.
genefu.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL genefu ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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 | 0.244 | 0.004 | 0.249 | |
boxplotplus2 | 0.006 | 0.004 | 0.009 | |
claudinLow | 0.956 | 0.020 | 0.978 | |
compareProtoCor | 1.435 | 0.036 | 1.474 | |
compute.pairw.cor.meta | 1.901 | 0.056 | 1.960 | |
compute.proto.cor.meta | 1.398 | 0.008 | 1.408 | |
cordiff.dep | 0.107 | 0.000 | 0.107 | |
endoPredict | 0.104 | 0.008 | 0.113 | |
fuzzy.ttest | 0.183 | 0.000 | 0.184 | |
gene70 | 0.259 | 0.016 | 0.275 | |
gene76 | 0.127 | 0.000 | 0.127 | |
geneid.map | 0.12 | 0.00 | 0.12 | |
genius | 0.268 | 0.000 | 0.268 | |
ggi | 0.115 | 0.004 | 0.119 | |
ihc4 | 0.102 | 0.000 | 0.102 | |
intrinsic.cluster | 0.449 | 0.000 | 0.442 | |
intrinsic.cluster.predict | 0.221 | 0.007 | 0.229 | |
map.datasets | 1.368 | 0.036 | 1.407 | |
molecular.subtyping | 2.926 | 0.040 | 2.986 | |
npi | 0.095 | 0.002 | 0.098 | |
oncotypedx | 0.117 | 0.001 | 0.117 | |
ovcAngiogenic | 0.123 | 0.000 | 0.123 | |
ovcCrijns | 0.135 | 0.008 | 0.143 | |
ovcTCGA | 0.277 | 0.004 | 0.282 | |
ovcYoshihara | 0.121 | 0.008 | 0.129 | |
pik3cags | 0.109 | 0.004 | 0.113 | |
power.cor | 0.001 | 0.000 | 0.001 | |
ps.cluster | 0.478 | 0.008 | 0.477 | |
read.m.file | 0.024 | 0.004 | 0.030 | |
rename.duplicate | 0.002 | 0.000 | 0.002 | |
rescale | 0.220 | 0.008 | 0.229 | |
rorS | 0.204 | 0.000 | 0.204 | |
setcolclass.df | 0.002 | 0.000 | 0.002 | |
sig.score | 0.119 | 0.004 | 0.123 | |
spearmanCI | 0.001 | 0.000 | 0.000 | |
st.gallen | 0.097 | 0.000 | 0.097 | |
stab.fs | 0.330 | 0.008 | 0.338 | |
stab.fs.ranking | 1.993 | 0.048 | 2.044 | |
strescR | 0.001 | 0.000 | 0.001 | |
subtype.cluster | 0.697 | 0.004 | 0.702 | |
subtype.cluster.predict | 0.267 | 0.008 | 0.275 | |
tamr13 | 0.138 | 0.000 | 0.138 | |
tbrm | 0 | 0 | 0 | |
weighted.meanvar | 0 | 0 | 0 | |
write.m.file | 0.004 | 0.000 | 0.003 | |