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BioC 3.4: CHECK report for MethTargetedNGS on morelia

This page was generated on 2017-04-15 16:26:30 -0400 (Sat, 15 Apr 2017).

Package 753/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethTargetedNGS 1.6.0
Muhammad Ahmer Jamil
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/MethTargetedNGS
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MethTargetedNGS
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MethTargetedNGS_1.6.0.tar.gz
StartedAt: 2017-04-15 04:52:39 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 04:54:17 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 97.9 seconds
RetCode: 0
Status:  OK 
CheckDir: MethTargetedNGS.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MethTargetedNGS_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/MethTargetedNGS.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethTargetedNGS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethTargetedNGS’ 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 ‘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
* 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 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
compare_samples 5.125  0.011   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 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/MethTargetedNGS.Rcheck/00check.log’
for details.


MethTargetedNGS.Rcheck/00install.out:

* 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
* DONE (MethTargetedNGS)

MethTargetedNGS.Rcheck/MethTargetedNGS-Ex.timings:

nameusersystemelapsed
bconv0.0030.0010.003
compare_samples5.1250.0115.145
fishertest_cpg4.6440.0194.682
hmmbuild0.0020.0000.002
methAlign2.5170.0052.527
methAvg2.4510.0072.478
methEntropy2.4810.0062.505
methHeatmap2.5800.0082.607
nhmmer0.0020.0000.003
odd_ratio4.6740.0124.734