Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:17 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 1517/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pigengene 1.31.0 (landing page) Habil Zare
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the Pigengene package: - 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: Pigengene |
Version: 1.31.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.31.0.tar.gz |
StartedAt: 2024-05-19 22:20:18 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 22:32:25 -0400 (Sun, 19 May 2024) |
EllapsedTime: 726.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Pigengene.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/Pigengene.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.31.0’ * 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 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 '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") one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db * checking Rd files ... NOTE checkRd: (-1) draw.bn.Rd:47: Lost braces 47 | rename the nodes name. See code{rename.node}.} | ^ checkRd: (-1) eigengenes33.Rd:21-22: Lost braces 21 | {A 202 by 34 matrix. | ^ checkRd: (-1) eigengenes33.Rd:25: Lost braces; missing escapes or markup? 25 | {A 164 by 34 matrix for MDS cases with columns similar to aml.} | ^ checkRd: (-1) eigengenes33.Rd:28: Lost braces; missing escapes or markup? 28 | {A numeric vector of length 9166 labeling members of each module. Named by Entrez ID.} | ^ checkRd: (-1) pigengene-class.Rd:22-23: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:24-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:27-34: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:35-36: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:37-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:40-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:51-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:53-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:55-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:59-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:68-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:72-74: Lost braces in \itemize; meant \describe ? * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed one.step.pigengene 100.315 2.925 103.339 Pigengene-package 96.094 2.749 98.983 get.enriched.pw 86.037 5.619 92.059 module.heatmap 36.369 2.481 38.906 learn.bn 19.848 0.472 20.328 make.filter 18.394 0.318 18.759 apply.filter 16.512 0.402 16.916 determine.modules 15.239 0.085 15.329 wgcna.one.step 15.085 0.044 15.131 make.decision.tree 13.221 0.877 14.163 combine.networks 13.351 0.120 13.510 compact.tree 12.065 0.965 13.087 pigengene 8.828 0.632 9.493 plot.pigengene 8.605 0.457 9.069 gene.mapping 8.119 0.767 11.886 compute.pigengene 8.326 0.524 8.852 project.eigen 8.189 0.476 8.669 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/Pigengene.Rcheck/00check.log’ for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 | 96.094 | 2.749 | 98.983 | |
aml | 0.153 | 0.007 | 0.160 | |
apply.filter | 16.512 | 0.402 | 16.916 | |
balance | 0.253 | 0.059 | 0.311 | |
calculate.beta | 0.893 | 0.035 | 0.927 | |
check.nas | 0.064 | 0.005 | 0.068 | |
check.pigengene.input | 0.063 | 0.004 | 0.068 | |
combine.networks | 13.351 | 0.120 | 13.510 | |
compact.tree | 12.065 | 0.965 | 13.087 | |
compute.pigengene | 8.326 | 0.524 | 8.852 | |
dcor.matrix | 0.167 | 0.015 | 0.182 | |
determine.modules | 15.239 | 0.085 | 15.329 | |
draw.bn | 0 | 0 | 0 | |
eigengenes33 | 0.091 | 0.007 | 0.098 | |
gene.mapping | 8.119 | 0.767 | 11.886 | |
get.enriched.pw | 86.037 | 5.619 | 92.059 | |
get.fitted.leaf | 0.449 | 0.036 | 0.505 | |
get.genes | 0.316 | 0.027 | 0.346 | |
get.used.features | 0.581 | 0.040 | 0.621 | |
learn.bn | 19.848 | 0.472 | 20.328 | |
make.decision.tree | 13.221 | 0.877 | 14.163 | |
make.filter | 18.394 | 0.318 | 18.759 | |
mds | 0.108 | 0.010 | 0.119 | |
message.if | 0.001 | 0.000 | 0.001 | |
module.heatmap | 36.369 | 2.481 | 38.906 | |
one.step.pigengene | 100.315 | 2.925 | 103.339 | |
pheatmap.type | 0.204 | 0.008 | 0.211 | |
pigengene | 8.828 | 0.632 | 9.493 | |
plot.pigengene | 8.605 | 0.457 | 9.069 | |
preds.at | 0.726 | 0.062 | 0.790 | |
project.eigen | 8.189 | 0.476 | 8.669 | |
pvalues.manova | 0.049 | 0.010 | 0.060 | |
save.if | 0.988 | 0.019 | 1.008 | |
wgcna.one.step | 15.085 | 0.044 | 15.131 | |