Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:37:45 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 794/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genefu 2.34.0 (landing page) Benjamin Haibe-Kains
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 2.34.0 |
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_2.34.0.tar.gz |
StartedAt: 2024-03-28 03:08:01 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 03:12:55 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 294.0 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_2.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/genefu.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * 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 ‘2.34.0’ * 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-3.18-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 R 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 ... OK * 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 in ‘inst/doc’ ... 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-3.18-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/4.3-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 | 0.378 | 0.024 | 0.417 | |
boxplotplus2 | 0.014 | 0.001 | 0.018 | |
claudinLow | 1.969 | 0.054 | 2.197 | |
compareProtoCor | 1.629 | 0.033 | 1.722 | |
compute.pairw.cor.meta | 2.307 | 0.052 | 2.632 | |
compute.proto.cor.meta | 1.496 | 0.027 | 1.721 | |
cordiff.dep | 0.188 | 0.008 | 0.212 | |
endoPredict | 0.194 | 0.013 | 0.227 | |
fuzzy.ttest | 0.277 | 0.022 | 0.323 | |
gene70 | 0.475 | 0.023 | 0.528 | |
gene76 | 0.221 | 0.013 | 0.254 | |
geneid.map | 0.245 | 0.023 | 0.301 | |
genius | 0.380 | 0.033 | 0.436 | |
ggi | 0.208 | 0.013 | 0.237 | |
ihc4 | 0.213 | 0.022 | 0.251 | |
intrinsic.cluster | 0.725 | 0.025 | 0.767 | |
intrinsic.cluster.predict | 0.354 | 0.015 | 0.395 | |
map.datasets | 1.410 | 0.027 | 1.482 | |
molecular.subtyping | 4.102 | 0.185 | 4.852 | |
npi | 0.222 | 0.019 | 0.273 | |
oncotypedx | 0.219 | 0.014 | 0.280 | |
ovcAngiogenic | 0.222 | 0.015 | 0.262 | |
ovcCrijns | 0.215 | 0.012 | 0.258 | |
ovcTCGA | 0.478 | 0.014 | 0.556 | |
ovcYoshihara | 0.244 | 0.012 | 0.280 | |
pik3cags | 0.216 | 0.012 | 0.255 | |
power.cor | 0.001 | 0.000 | 0.002 | |
ps.cluster | 0.804 | 0.022 | 0.872 | |
read.m.file | 0.039 | 0.005 | 0.049 | |
rename.duplicate | 0.002 | 0.001 | 0.004 | |
rescale | 0.421 | 0.014 | 0.499 | |
rorS | 0.402 | 0.013 | 0.459 | |
setcolclass.df | 0.002 | 0.000 | 0.003 | |
sig.score | 0.220 | 0.013 | 0.253 | |
spearmanCI | 0.001 | 0.001 | 0.001 | |
st.gallen | 0.191 | 0.012 | 0.236 | |
stab.fs | 0.294 | 0.017 | 0.349 | |
stab.fs.ranking | 1.680 | 0.114 | 2.047 | |
strescR | 0.001 | 0.001 | 0.003 | |
subtype.cluster | 1.147 | 0.094 | 1.415 | |
subtype.cluster.predict | 0.488 | 0.033 | 0.593 | |
tamr13 | 0.238 | 0.014 | 0.274 | |
tbrm | 0.001 | 0.000 | 0.001 | |
weighted.meanvar | 0.000 | 0.000 | 0.001 | |
write.m.file | 0.006 | 0.005 | 0.011 | |