Habil Zare
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Pigengene |
| Branch: RELEASE_3_8 |
| Last Commit: 59ee84d |
| Last Changed Date: 2019-01-04 13:06:36 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:39 -0400 (Tue, 16 Apr 2019).
| Package 1160/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Pigengene 1.8.1 Habil Zare
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: Pigengene |
| Version: 1.8.1 |
| 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_1.8.1.tar.gz |
| StartedAt: 2019-04-16 01:55:11 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:02:10 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 419.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Pigengene.Rcheck |
| Warnings: 1 |
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### Running 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_1.8.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Pigengene.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.1’
* 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 ... WARNING
Missing link or links in documentation object 'Pigengene-package.Rd':
‘[WGCNA]{WGCNA-package}’
Missing link or links in documentation object 'calculate.beta.Rd':
‘[WGCNA]{WGCNA-package}’
Missing link or links in documentation object 'compute.pigengene.Rd':
‘[WGCNA]{WGCNA-package}’
Missing link or links in documentation object 'learn.bn.Rd':
‘[WGCNA]{WGCNA-package}’
Missing link or links in documentation object 'one.step.pigengene.Rd':
‘[WGCNA]{WGCNA-package}’
Missing link or links in documentation object 'wgcna.one.step.Rd':
‘[WGCNA]{WGCNA-package}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 or elapsed time > 5s
user system elapsed
Pigengene-package 70.585 4.260 75.234
one.step.pigengene 65.580 4.431 69.917
module.heatmap 25.684 2.212 28.385
make.decision.tree 16.859 1.897 18.917
compact.tree 15.682 1.969 17.689
plot.pigengene 8.696 0.771 9.462
compute.pigengene 8.111 0.819 8.941
project.eigen 7.253 0.712 7.951
wgcna.one.step 7.726 0.091 7.863
pigengene 6.834 0.702 7.573
* 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-3.8-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/3.5/Resources/library’ * installing *source* package ‘Pigengene’ ... ** 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 * DONE (Pigengene)
Pigengene.Rcheck/Pigengene-Ex.timings
| name | user | system | elapsed | |
| Pigengene-package | 70.585 | 4.260 | 75.234 | |
| aml | 0.387 | 0.022 | 0.403 | |
| balance | 0.843 | 0.150 | 0.997 | |
| calculate.beta | 0.636 | 0.096 | 0.736 | |
| check.nas | 0.064 | 0.009 | 0.073 | |
| check.pigengene.input | 0.045 | 0.005 | 0.050 | |
| compact.tree | 15.682 | 1.969 | 17.689 | |
| compute.pigengene | 8.111 | 0.819 | 8.941 | |
| dcor.matrix | 0.191 | 0.049 | 0.245 | |
| draw.bn | 0.001 | 0.000 | 0.000 | |
| eigengenes33 | 0.140 | 0.003 | 0.145 | |
| gene.mapping | 1.521 | 0.149 | 1.679 | |
| get.fitted.leaf | 0.937 | 0.074 | 1.005 | |
| get.genes | 0.860 | 0.073 | 0.927 | |
| get.used.features | 0.853 | 0.075 | 0.925 | |
| learn.bn | 4.697 | 0.149 | 4.818 | |
| make.decision.tree | 16.859 | 1.897 | 18.917 | |
| mds | 0.148 | 0.008 | 0.158 | |
| module.heatmap | 25.684 | 2.212 | 28.385 | |
| one.step.pigengene | 65.580 | 4.431 | 69.917 | |
| pheatmap.type | 0.616 | 0.022 | 0.637 | |
| pigengene | 6.834 | 0.702 | 7.573 | |
| plot.pigengene | 8.696 | 0.771 | 9.462 | |
| preds.at | 0.920 | 0.081 | 0.992 | |
| project.eigen | 7.253 | 0.712 | 7.951 | |
| pvalues.manova | 0.134 | 0.017 | 0.145 | |
| wgcna.one.step | 7.726 | 0.091 | 7.863 | |