Habil Zare
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/Pigengene |
| Branch: RELEASE_3_7 |
| Last Commit: f0c7998 |
| Last Changed Date: 2018-04-30 10:35:42 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:29:02 -0400 (Wed, 17 Oct 2018).
| Package 1097/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Pigengene 1.6.0 Habil Zare
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: Pigengene |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Pigengene_1.6.0.tar.gz |
| StartedAt: 2018-10-16 02:42:30 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 02:47:07 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 277.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Pigengene.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Pigengene_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/Pigengene.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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.
':::' call which should be '::': ‘C50:::as.party.C5.0’
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 ... NOTE
Found the following possibly unsafe calls:
File ‘Pigengene/R/bn.calculation.R’:
assignInNamespace("supported.clusters", fixArgs, "bnlearn")
check.pigengene.input: no visible global function definition for
‘setNames’
welch.pvalue: no visible global function definition for ‘as.formula’
welch.pvalue: no visible global function definition for ‘oneway.test’
Undefined global functions or variables:
as.formula oneway.test setNames
Consider adding
importFrom("stats", "as.formula", "oneway.test", "setNames")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Pigengene-package 50.300 0.568 50.941
one.step.pigengene 50.196 0.532 50.775
module.heatmap 13.268 0.020 13.299
make.decision.tree 10.840 0.076 10.936
compact.tree 9.776 0.024 9.828
wgcna.one.step 8.528 0.004 8.539
compute.pigengene 5.092 0.024 5.145
* 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
‘/home/biocbuild/bbs-3.7-bioc/meat/Pigengene.Rcheck/00check.log’
for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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 | 50.300 | 0.568 | 50.941 | |
| aml | 0.160 | 0.000 | 0.161 | |
| balance | 0.292 | 0.040 | 0.331 | |
| calculate.beta | 2.708 | 0.040 | 2.747 | |
| check.nas | 0.044 | 0.000 | 0.045 | |
| check.pigengene.input | 0.040 | 0.008 | 0.046 | |
| compact.tree | 9.776 | 0.024 | 9.828 | |
| compute.pigengene | 5.092 | 0.024 | 5.145 | |
| dcor.matrix | 0.144 | 0.004 | 0.150 | |
| draw.bn | 0 | 0 | 0 | |
| eigengenes33 | 0.096 | 0.004 | 0.101 | |
| gene.mapping | 0.936 | 0.060 | 1.000 | |
| get.fitted.leaf | 0.544 | 0.008 | 0.551 | |
| get.genes | 0.500 | 0.000 | 0.503 | |
| get.used.features | 0.524 | 0.000 | 0.525 | |
| learn.bn | 3.924 | 0.176 | 4.122 | |
| make.decision.tree | 10.840 | 0.076 | 10.936 | |
| mds | 0.100 | 0.000 | 0.101 | |
| module.heatmap | 13.268 | 0.020 | 13.299 | |
| one.step.pigengene | 50.196 | 0.532 | 50.775 | |
| pheatmap.type | 0.260 | 0.000 | 0.264 | |
| pigengene | 4.652 | 0.092 | 4.748 | |
| plot.pigengene | 4.776 | 0.080 | 4.856 | |
| preds.at | 0.616 | 0.008 | 0.626 | |
| project.eigen | 4.292 | 0.036 | 4.329 | |
| pvalues.manova | 0.108 | 0.004 | 0.110 | |
| wgcna.one.step | 8.528 | 0.004 | 8.539 | |