Habil Zare
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Pigengene |
| Branch: RELEASE_3_9 |
| Last Commit: fb16e07 |
| Last Changed Date: 2019-05-02 11:54:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:58:05 -0400 (Wed, 16 Oct 2019).
| Package 1214/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Pigengene 1.10.0 Habil Zare
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Pigengene |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.10.0.tar.gz |
| StartedAt: 2019-10-16 05:34:08 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:44:16 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 607.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Pigengene.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Pigengene.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.10.0’
* 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 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
'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")
* 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 ... NOTE
Output for data("pigengene", package = "Pigengene"):
* 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 or elapsed time > 5s
user system elapsed
one.step.pigengene 89.127 7.109 96.061
Pigengene-package 88.633 7.398 95.986
module.heatmap 30.212 4.561 35.253
make.decision.tree 20.875 3.670 24.550
compact.tree 19.163 4.344 23.518
plot.pigengene 14.171 1.667 15.769
compute.pigengene 12.315 1.549 13.868
project.eigen 11.615 1.433 13.017
pigengene 10.619 1.375 11.995
wgcna.one.step 10.200 0.205 10.391
gene.mapping 8.528 0.884 28.170
learn.bn 5.487 0.210 5.674
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/Pigengene.Rcheck/00check.log’
for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 | 88.633 | 7.398 | 95.986 | |
| aml | 0.437 | 0.033 | 0.465 | |
| balance | 3.138 | 0.317 | 3.455 | |
| calculate.beta | 0.751 | 0.119 | 0.870 | |
| check.nas | 0.070 | 0.018 | 0.088 | |
| check.pigengene.input | 0.065 | 0.014 | 0.080 | |
| compact.tree | 19.163 | 4.344 | 23.518 | |
| compute.pigengene | 12.315 | 1.549 | 13.868 | |
| dcor.matrix | 0.291 | 0.121 | 0.414 | |
| draw.bn | 0.001 | 0.001 | 0.000 | |
| eigengenes33 | 0.177 | 0.007 | 0.185 | |
| gene.mapping | 8.528 | 0.884 | 28.170 | |
| get.fitted.leaf | 1.036 | 0.128 | 1.154 | |
| get.genes | 0.951 | 0.113 | 1.066 | |
| get.used.features | 1.013 | 0.105 | 1.122 | |
| learn.bn | 5.487 | 0.210 | 5.674 | |
| make.decision.tree | 20.875 | 3.670 | 24.550 | |
| mds | 0.126 | 0.011 | 0.139 | |
| module.heatmap | 30.212 | 4.561 | 35.253 | |
| one.step.pigengene | 89.127 | 7.109 | 96.061 | |
| pheatmap.type | 0.709 | 0.033 | 0.743 | |
| pigengene | 10.619 | 1.375 | 11.995 | |
| plot.pigengene | 14.171 | 1.667 | 15.769 | |
| preds.at | 1.262 | 0.162 | 1.424 | |
| project.eigen | 11.615 | 1.433 | 13.017 | |
| pvalues.manova | 0.143 | 0.023 | 0.158 | |
| wgcna.one.step | 10.200 | 0.205 | 10.391 | |