Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-17 12:22 -0400 (Mon, 17 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4685 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4400 |
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 779/2242 | 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 | |||||||||
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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings genefu_2.37.0.tar.gz |
StartedAt: 2024-06-16 23:19:39 -0400 (Sun, 16 Jun 2024) |
EndedAt: 2024-06-16 23:22:36 -0400 (Sun, 16 Jun 2024) |
EllapsedTime: 177.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: genefu.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings genefu_2.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/genefu.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 ‘/home/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 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/genefu.Rcheck/00check.log’ for details.
genefu.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL genefu ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 | 0.200 | 0.008 | 0.208 | |
boxplotplus2 | 0.008 | 0.000 | 0.008 | |
claudinLow | 0.625 | 0.016 | 0.641 | |
compareProtoCor | 1.181 | 0.052 | 1.233 | |
compute.pairw.cor.meta | 1.320 | 0.064 | 1.384 | |
compute.proto.cor.meta | 1.113 | 0.008 | 1.120 | |
cordiff.dep | 0.11 | 0.00 | 0.11 | |
endoPredict | 0.110 | 0.004 | 0.114 | |
fuzzy.ttest | 0.084 | 0.000 | 0.083 | |
gene70 | 0.261 | 0.008 | 0.269 | |
gene76 | 0.118 | 0.004 | 0.122 | |
geneid.map | 0.108 | 0.004 | 0.112 | |
genius | 0.189 | 0.008 | 0.198 | |
ggi | 0.108 | 0.000 | 0.108 | |
ihc4 | 0.099 | 0.000 | 0.099 | |
intrinsic.cluster | 0.347 | 0.008 | 0.341 | |
intrinsic.cluster.predict | 0.159 | 0.000 | 0.158 | |
map.datasets | 1.031 | 0.004 | 1.034 | |
molecular.subtyping | 2.208 | 0.084 | 2.295 | |
npi | 0.102 | 0.000 | 0.101 | |
oncotypedx | 0.112 | 0.000 | 0.112 | |
ovcAngiogenic | 0.128 | 0.008 | 0.135 | |
ovcCrijns | 0.113 | 0.004 | 0.117 | |
ovcTCGA | 0.207 | 0.016 | 0.223 | |
ovcYoshihara | 0.107 | 0.004 | 0.111 | |
pik3cags | 0.105 | 0.004 | 0.109 | |
power.cor | 0.001 | 0.000 | 0.000 | |
ps.cluster | 0.335 | 0.016 | 0.337 | |
read.m.file | 0.017 | 0.000 | 0.018 | |
rename.duplicate | 0.001 | 0.000 | 0.001 | |
rescale | 0.223 | 0.004 | 0.228 | |
rorS | 0.166 | 0.000 | 0.166 | |
setcolclass.df | 0.002 | 0.000 | 0.002 | |
sig.score | 0.110 | 0.004 | 0.114 | |
spearmanCI | 0 | 0 | 0 | |
st.gallen | 0.095 | 0.004 | 0.099 | |
stab.fs | 0.101 | 0.000 | 0.101 | |
stab.fs.ranking | 0.489 | 0.032 | 0.521 | |
strescR | 0 | 0 | 0 | |
subtype.cluster | 0.637 | 0.016 | 0.654 | |
subtype.cluster.predict | 0.269 | 0.016 | 0.285 | |
tamr13 | 0.123 | 0.007 | 0.130 | |
tbrm | 0 | 0 | 0 | |
weighted.meanvar | 0 | 0 | 0 | |
write.m.file | 0.004 | 0.000 | 0.004 | |