Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:40 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
To the developers/maintainers of the Pigengene package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pigengene.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1506/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pigengene 1.25.16 (landing page) Habil Zare
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: Pigengene |
Version: 1.25.16 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Pigengene_1.25.16.tar.gz |
StartedAt: 2023-04-12 08:23:04 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 08:38:16 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 912.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Pigengene.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Pigengene_1.25.16.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Pigengene.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.25.16’ * 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 ‘Pigengene’ can be installed ... OK * checking installed package size ... OK * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘Pigengene/R/bn.calculation.R’: assignInNamespace("supported.clusters", fixArgs, "bnlearn") compute.pigengene: no visible global function definition for ‘prcomp’ one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db prcomp Consider adding importFrom("stats", "prcomp") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) get.enriched.pw.Rd:71: Escaped LaTeX specials: \_ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed get.enriched.pw 93.338 2.894 96.776 one.step.pigengene 91.687 0.677 92.399 Pigengene-package 79.895 1.452 81.350 module.heatmap 50.477 0.394 51.265 learn.bn 20.773 0.016 20.790 make.filter 18.961 0.208 19.309 combine.networks 17.156 0.125 17.281 apply.filter 16.585 0.180 16.765 determine.modules 16.503 0.081 16.585 wgcna.one.step 16.016 0.144 16.160 make.decision.tree 10.824 0.016 10.840 compact.tree 10.301 0.068 10.369 gene.mapping 7.256 0.363 34.440 pigengene 6.986 0.100 7.086 compute.pigengene 6.953 0.124 7.077 plot.pigengene 6.284 0.036 6.321 project.eigen 6.078 0.008 6.086 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Pigengene_inference.Rnw’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/Pigengene.Rcheck/00check.log’ for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘Pigengene’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Pigengene)
Pigengene.Rcheck/Pigengene-Ex.timings
name | user | system | elapsed | |
Pigengene-package | 79.895 | 1.452 | 81.350 | |
aml | 0.162 | 0.000 | 0.162 | |
apply.filter | 16.585 | 0.180 | 16.765 | |
balance | 0.445 | 0.060 | 0.505 | |
calculate.beta | 0.853 | 0.016 | 0.870 | |
check.nas | 0.060 | 0.004 | 0.065 | |
check.pigengene.input | 0.061 | 0.004 | 0.066 | |
combine.networks | 17.156 | 0.125 | 17.281 | |
compact.tree | 10.301 | 0.068 | 10.369 | |
compute.pigengene | 6.953 | 0.124 | 7.077 | |
dcor.matrix | 0.142 | 0.004 | 0.146 | |
determine.modules | 16.503 | 0.081 | 16.585 | |
draw.bn | 0 | 0 | 0 | |
eigengenes33 | 0.089 | 0.000 | 0.089 | |
gene.mapping | 7.256 | 0.363 | 34.440 | |
get.enriched.pw | 93.338 | 2.894 | 96.776 | |
get.fitted.leaf | 0.504 | 0.000 | 0.504 | |
get.genes | 0.479 | 0.000 | 0.479 | |
get.used.features | 0.568 | 0.000 | 0.569 | |
learn.bn | 20.773 | 0.016 | 20.790 | |
make.decision.tree | 10.824 | 0.016 | 10.840 | |
make.filter | 18.961 | 0.208 | 19.309 | |
mds | 0.127 | 0.000 | 0.128 | |
message.if | 0.000 | 0.000 | 0.001 | |
module.heatmap | 50.477 | 0.394 | 51.265 | |
one.step.pigengene | 91.687 | 0.677 | 92.399 | |
pheatmap.type | 0.190 | 0.000 | 0.191 | |
pigengene | 6.986 | 0.100 | 7.086 | |
plot.pigengene | 6.284 | 0.036 | 6.321 | |
preds.at | 0.705 | 0.004 | 0.709 | |
project.eigen | 6.078 | 0.008 | 6.086 | |
pvalues.manova | 0.063 | 0.004 | 0.067 | |
save.if | 0.897 | 0.000 | 0.897 | |
wgcna.one.step | 16.016 | 0.144 | 16.160 | |