Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-26 11:38 -0400 (Wed, 26 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4691 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4405 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4355 |
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 779/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genefu 2.37.0 (landing page) Benjamin Haibe-Kains
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
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: 2.37.0 |
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_2.37.0.tar.gz |
StartedAt: 2024-06-25 20:26:43 -0400 (Tue, 25 Jun 2024) |
EndedAt: 2024-06-25 20:29:28 -0400 (Tue, 25 Jun 2024) |
EllapsedTime: 164.4 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_2.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/genefu.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘genefu/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘genefu’ version ‘2.37.0’ * 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-3.20-bioc/meat/genefu.Rcheck/00install.out’ for details. * checking installed package size ... NOTE 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘genefu’ ... ** 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 | 0.245 | 0.012 | 0.259 | |
boxplotplus2 | 0.007 | 0.001 | 0.008 | |
claudinLow | 0.750 | 0.020 | 0.777 | |
compareProtoCor | 1.364 | 0.023 | 1.403 | |
compute.pairw.cor.meta | 1.615 | 0.027 | 1.657 | |
compute.proto.cor.meta | 1.224 | 0.018 | 1.255 | |
cordiff.dep | 0.125 | 0.003 | 0.129 | |
endoPredict | 0.130 | 0.005 | 0.136 | |
fuzzy.ttest | 0.112 | 0.009 | 0.122 | |
gene70 | 0.325 | 0.023 | 0.355 | |
gene76 | 0.147 | 0.007 | 0.155 | |
geneid.map | 0.136 | 0.007 | 0.144 | |
genius | 0.242 | 0.019 | 0.262 | |
ggi | 0.127 | 0.007 | 0.138 | |
ihc4 | 0.115 | 0.007 | 0.122 | |
intrinsic.cluster | 0.420 | 0.018 | 0.425 | |
intrinsic.cluster.predict | 0.183 | 0.008 | 0.195 | |
map.datasets | 1.281 | 0.022 | 1.313 | |
molecular.subtyping | 2.738 | 0.114 | 2.882 | |
npi | 0.105 | 0.006 | 0.112 | |
oncotypedx | 0.133 | 0.006 | 0.140 | |
ovcAngiogenic | 0.155 | 0.014 | 0.172 | |
ovcCrijns | 0.122 | 0.006 | 0.128 | |
ovcTCGA | 0.250 | 0.006 | 0.258 | |
ovcYoshihara | 0.126 | 0.006 | 0.132 | |
pik3cags | 0.124 | 0.007 | 0.134 | |
power.cor | 0.001 | 0.000 | 0.001 | |
ps.cluster | 0.425 | 0.016 | 0.423 | |
read.m.file | 0.022 | 0.003 | 0.026 | |
rename.duplicate | 0.002 | 0.001 | 0.003 | |
rescale | 0.270 | 0.010 | 0.284 | |
rorS | 0.212 | 0.008 | 0.222 | |
setcolclass.df | 0.002 | 0.000 | 0.002 | |
sig.score | 0.130 | 0.007 | 0.139 | |
spearmanCI | 0.000 | 0.000 | 0.001 | |
st.gallen | 0.120 | 0.007 | 0.128 | |
stab.fs | 0.133 | 0.010 | 0.142 | |
stab.fs.ranking | 0.624 | 0.038 | 0.670 | |
strescR | 0.001 | 0.001 | 0.001 | |
subtype.cluster | 0.709 | 0.050 | 0.770 | |
subtype.cluster.predict | 0.328 | 0.018 | 0.354 | |
tamr13 | 0.170 | 0.008 | 0.179 | |
tbrm | 0.001 | 0.000 | 0.000 | |
weighted.meanvar | 0.001 | 0.001 | 0.000 | |
write.m.file | 0.005 | 0.003 | 0.007 | |