BioC 3.6: CHECK report for MethTargetedNGS on tokay1
This page was generated on 2017-08-16 13:34:30 -0400 (Wed, 16 Aug 2017).
MethTargetedNGS 1.9.0
Muhammad Ahmer Jamil
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MethTargetedNGS | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: MethTargetedNGS
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| Version: 1.9.0
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| Command: rm -rf MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && mkdir MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethTargetedNGS.buildbin-libdir MethTargetedNGS_1.9.0.tar.gz >MethTargetedNGS.Rcheck\00install.out 2>&1 && cp MethTargetedNGS.Rcheck\00install.out MethTargetedNGS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MethTargetedNGS.buildbin-libdir --install="check:MethTargetedNGS-install.out" --force-multiarch --no-vignettes --timings MethTargetedNGS_1.9.0.tar.gz
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| StartedAt: 2017-08-16 00:46:37 -0400 (Wed, 16 Aug 2017)
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| EndedAt: 2017-08-16 00:49:01 -0400 (Wed, 16 Aug 2017)
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| EllapsedTime: 143.8 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: MethTargetedNGS.Rcheck
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| Warnings: 0
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Command output
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### Running command:
###
### rm -rf MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && mkdir MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethTargetedNGS.buildbin-libdir MethTargetedNGS_1.9.0.tar.gz >MethTargetedNGS.Rcheck\00install.out 2>&1 && cp MethTargetedNGS.Rcheck\00install.out MethTargetedNGS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MethTargetedNGS.buildbin-libdir --install="check:MethTargetedNGS-install.out" --force-multiarch --no-vignettes --timings MethTargetedNGS_1.9.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MethTargetedNGS.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MethTargetedNGS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethTargetedNGS' version '1.9.0'
* 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 whether package 'MethTargetedNGS' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compare_samples: no visible global function definition for 'par'
compare_samples: no visible global function definition for 'plot'
compare_samples: no visible global function definition for 'lines'
fishertest_cpg: no visible global function definition for 'fisher.test'
fishertest_cpg: no visible global function definition for 'p.adjust'
fishertest_cpg: no visible global function definition for 'barplot'
fishertest_cpg: no visible global function definition for 'abline'
methAlign: no visible global function definition for 'subject'
methAlign: no visible global function definition for 'pattern'
nhmmer: no visible global function definition for 'read.table'
nhmmer: no visible global function definition for 'setNames'
Undefined global functions or variables:
abline barplot fisher.test lines p.adjust par pattern plot read.table
setNames subject
Consider adding
importFrom("graphics", "abline", "barplot", "lines", "par", "plot")
importFrom("stats", "fisher.test", "p.adjust", "setNames")
importFrom("utils", "read.table")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fishertest_cpg 6.20 0.02 6.22
compare_samples 5.77 0.00 5.77
** running examples for arch 'x64' ... OK
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/MethTargetedNGS.Rcheck/00check.log'
for details.
MethTargetedNGS.Rcheck/00install.out:
install for i386
* installing *source* package 'MethTargetedNGS' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'MethTargetedNGS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethTargetedNGS' as MethTargetedNGS_1.9.0.zip
* DONE (MethTargetedNGS)
MethTargetedNGS.Rcheck/examples_i386/MethTargetedNGS-Ex.timings:
| name | user | system | elapsed
|
| bconv | 0 | 0 | 0 |
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| compare_samples | 5.77 | 0.00 | 5.77 |
|
| fishertest_cpg | 6.20 | 0.02 | 6.22 |
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| hmmbuild | 0 | 0 | 0 |
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| methAlign | 2.45 | 0.00 | 2.46 |
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| methAvg | 1.95 | 0.00 | 1.95 |
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| methEntropy | 1.94 | 0.00 | 1.94 |
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| methHeatmap | 2.00 | 0.02 | 2.01 |
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| nhmmer | 0 | 0 | 0 |
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| odd_ratio | 4.34 | 0.00 | 4.35 |
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MethTargetedNGS.Rcheck/examples_x64/MethTargetedNGS-Ex.timings:
| name | user | system | elapsed
|
| bconv | 0.01 | 0.00 | 0.02 |
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| compare_samples | 4.24 | 0.00 | 4.23 |
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| fishertest_cpg | 3.94 | 0.00 | 3.94 |
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| hmmbuild | 0.02 | 0.00 | 0.01 |
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| methAlign | 1.86 | 0.00 | 1.86 |
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| methAvg | 1.92 | 0.00 | 1.92 |
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| methEntropy | 2.06 | 0.00 | 2.07 |
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| methHeatmap | 2 | 0 | 2 |
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| nhmmer | 0 | 0 | 0 |
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| odd_ratio | 4.23 | 0.00 | 4.24 |
|