Habil Zare
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/Pigengene |
| Branch: RELEASE_3_6 |
| Last Commit: 7b61c56 |
| Last Changed Date: 2018-03-18 09:41:27 -0400 (Sun, 18 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:43:02 -0400 (Thu, 12 Apr 2018).
| Package 1040/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Pigengene 1.4.20 Habil Zare
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: Pigengene |
| Version: 1.4.20 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pigengene_1.4.20.tar.gz |
| StartedAt: 2018-04-12 07:42:14 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 07:48:55 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 401.3 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 --no-vignettes --timings Pigengene_1.4.20.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Pigengene.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.20’
* 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.
Unexported object imported by a ':::' call: ‘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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Pigengene-package 66.389 2.890 70.601
one.step.pigengene 62.585 3.141 67.146
module.heatmap 22.713 1.551 25.165
make.decision.tree 15.561 1.035 16.885
compact.tree 15.431 0.734 16.431
compute.pigengene 8.969 0.598 9.783
plot.pigengene 8.686 0.800 9.699
project.eigen 6.931 0.742 7.818
pigengene 6.280 0.798 7.224
wgcna.one.step 6.960 0.088 7.170
learn.bn 5.295 0.082 5.507
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/Pigengene.Rcheck/00check.log’
for details.
Pigengene.Rcheck/00install.out
* installing *source* package ‘Pigengene’ ... ** R ** data ** inst ** preparing 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 | 66.389 | 2.890 | 70.601 | |
| aml | 0.145 | 0.006 | 0.154 | |
| balance | 0.654 | 0.137 | 0.803 | |
| calculate.beta | 2.474 | 0.041 | 2.557 | |
| check.nas | 0.052 | 0.004 | 0.058 | |
| check.pigengene.input | 0.053 | 0.004 | 0.059 | |
| compact.tree | 15.431 | 0.734 | 16.431 | |
| compute.pigengene | 8.969 | 0.598 | 9.783 | |
| dcor.matrix | 0.190 | 0.038 | 0.231 | |
| draw.bn | 0.000 | 0.001 | 0.001 | |
| eigengenes33 | 0.120 | 0.003 | 0.126 | |
| gene.mapping | 1.622 | 0.104 | 1.744 | |
| get.fitted.leaf | 0.735 | 0.044 | 0.792 | |
| get.genes | 0.737 | 0.044 | 0.796 | |
| get.used.features | 0.949 | 0.052 | 1.022 | |
| learn.bn | 5.295 | 0.082 | 5.507 | |
| make.decision.tree | 15.561 | 1.035 | 16.885 | |
| mds | 0.126 | 0.006 | 0.133 | |
| module.heatmap | 22.713 | 1.551 | 25.165 | |
| one.step.pigengene | 62.585 | 3.141 | 67.146 | |
| pheatmap.type | 0.265 | 0.006 | 0.272 | |
| pigengene | 6.280 | 0.798 | 7.224 | |
| plot.pigengene | 8.686 | 0.800 | 9.699 | |
| preds.at | 0.931 | 0.058 | 1.010 | |
| project.eigen | 6.931 | 0.742 | 7.818 | |
| pvalues.manova | 0.028 | 0.001 | 0.033 | |
| wgcna.one.step | 6.960 | 0.088 | 7.170 | |