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BioC 3.5: CHECK report for TCseq on toluca2

This page was generated on 2017-04-23 14:42:32 -0400 (Sun, 23 Apr 2017).

Package 1306/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCseq 0.99.9
Mengjun Wu
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TCseq
Last Changed Rev: 125426 / Revision: 129046
Last Changed Date: 2016-12-23 15:17:03 -0500 (Fri, 23 Dec 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCseq
Version: 0.99.9
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCseq_0.99.9.tar.gz
StartedAt: 2017-04-23 10:39:20 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 10:44:07 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 286.4 seconds
RetCode: 0
Status:  OK 
CheckDir: TCseq.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 TCseq_0.99.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TCseq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCseq’ version ‘0.99.9’
* 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 ‘TCseq’ 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
DBresult: no visible global function definition for ‘as’
DBresult.cluster: no visible global function definition for ‘as’
TCA: no visible global function definition for ‘is’
TCA: no visible global function definition for ‘as’
TCAFromSummarizedExperiment: no visible global function definition for
  ‘is’
TCAFromSummarizedExperiment: no visible global function definition for
  ‘as’
countReads: no visible global function definition for
  ‘createAnnotationFile’
countReads: no visible global function definition for ‘featureCounts’
timeclustplot: no visible binding for global variable ‘group’
timecourseTable: no visible global function definition for ‘as’
Undefined global functions or variables:
  as createAnnotationFile featureCounts group is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
DBresult      4.950  0.134   7.784
timeclustplot 4.646  0.017   6.941
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/TCseq.Rcheck/00check.log’
for details.


TCseq.Rcheck/00install.out:

* installing *source* package ‘TCseq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCseq)

TCseq.Rcheck/TCseq-Ex.timings:

nameusersystemelapsed
DBanalysis2.1460.0532.873
DBresult4.9500.1347.784
TCA0.1270.0010.204
TCA.accessors0.1120.0330.219
counts0.0850.0020.130
countsTable0.0010.0000.002
experiment0.0010.0000.007
experiment_BAMfile0.0020.0010.002
genomicIntervals0.0020.0010.003
peakreference0.0760.0000.114
tca_ATAC0.0020.0000.008
timeclust0.2290.0010.345
timeclustplot4.6460.0176.941
timecourseTable1.2310.0431.869