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BioC 3.4: CHECK report for biobroom on moscato1

This page was generated on 2016-09-21 03:47:44 -0700 (Wed, 21 Sep 2016).

Package 105/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biobroom 1.5.2
John D. Storey and Andrew J. Bass
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/biobroom
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: biobroom
Version: 1.5.2
Command: rm -rf biobroom.buildbin-libdir biobroom.Rcheck && mkdir biobroom.buildbin-libdir biobroom.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biobroom.buildbin-libdir biobroom_1.5.2.tar.gz >biobroom.Rcheck\00install.out 2>&1 && cp biobroom.Rcheck\00install.out biobroom-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=biobroom.buildbin-libdir --install="check:biobroom-install.out" --force-multiarch --no-vignettes --timings biobroom_1.5.2.tar.gz
StartedAt: 2016-09-20 04:36:48 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:39:47 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 178.9 seconds
RetCode: 0
Status:  OK  
CheckDir: biobroom.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf biobroom.buildbin-libdir biobroom.Rcheck && mkdir biobroom.buildbin-libdir biobroom.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biobroom.buildbin-libdir biobroom_1.5.2.tar.gz >biobroom.Rcheck\00install.out 2>&1 && cp biobroom.Rcheck\00install.out biobroom-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=biobroom.buildbin-libdir --install="check:biobroom-install.out" --force-multiarch --no-vignettes --timings biobroom_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/biobroom.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biobroom/DESCRIPTION' ... OK
* this is package 'biobroom' version '1.5.2'
* 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 'biobroom' 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 ... NOTE
'library' or 'require' call to 'DESeq2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: 'dplyr::tbl_dt'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
finish: no visible global function definition for 'tbl_dt'
glance.DGEExact: no visible global function definition for 'p.adjust'
glance.GRanges: no visible binding for global variable 'gr'
glance.GRangesList: no visible binding for global variable 'gr'
makeExampleDataSet: no visible global function definition for
  'estimateSizeFactors'
makeExampleDataSet: no visible global function definition for 'counts'
makeExampleDataSet: no visible global function definition for 'colData'
makeExampleDataSet: no visible global function definition for
  'seqnames'
makeExampleDataSet: no visible global function definition for
  'rowRanges'
makeExampleDataSet: no visible global function definition for 'start'
makeExampleDataSet: no visible global function definition for 'end'
makeExampleDataSet: no visible global function definition for 'DGEList'
makeExampleDataSet: no visible global function definition for
  'calcNormFactors'
makeExampleDataSet: no visible global function definition for
  'model.matrix'
makeExampleDataSet: no visible global function definition for 'design'
makeExampleDataSet: no visible global function definition for
  'voomWithQualityWeights'
makeExampleDataSet: no visible global function definition for 'voom'
makeExampleDataSet: no visible global function definition for 'pData<-'
makeExampleDataSet: no visible global function definition for 'fData<-'
makeExampleDataSet: no visible global function definition for 'is'
tidy.DESeqDataSet: no visible binding for global variable 'term'
tidy.DESeqDataSet: no visible binding for global variable '.'
tidy.DESeqDataSet: no visible global function definition for 'counts'
tidy.DESeqDataSet: no visible binding for global variable 'gene'
tidy.DGEList: no visible binding for global variable 'gene'
tidy.EList: no visible global function definition for 'setNames'
tidy.ExpressionSet: no visible binding for global variable 'value'
tidy.ExpressionSet: no visible binding for global variable 'gene'
tidy.ExpressionSet: no visible global function definition for 'pData'
tidy.MArrayLM: no visible binding for global variable 'term'
tidy.MArrayLM: no visible binding for global variable 'estimate'
tidy.MArrayLM: no visible binding for global variable 'gene'
tidy.MSnSet: no visible binding for global variable 'sample.id'
tidy.MSnSet: no visible binding for global variable 'value'
tidy.MSnSet: no visible binding for global variable 'protein'
tidy.MSnSet: no visible global function definition for 'pData'
tidy.RangedSummarizedExperiment: no visible binding for global variable
  'value'
tidy.RangedSummarizedExperiment: no visible binding for global variable
  'gene'
tidy.RangedSummarizedExperiment: no visible global function definition
  for 'colData'
tidy.deSet: no visible global function definition for 'exprs<-'
tidy.deSet: no visible binding for global variable 'value'
tidy.deSet: no visible binding for global variable 'gene'
tidy.deSet: no visible global function definition for 'pData'
tidy.qvalue: no visible binding for global variable 'smoothed'
tidy.qvalue: no visible binding for global variable 'pi0'
tidy.qvalue: no visible binding for global variable 'lambda'
tidy_matrix: no visible binding for global variable 'value'
tidy_matrix: no visible binding for global variable 'gene'
Undefined global functions or variables:
  . DGEList calcNormFactors colData counts design end estimate
  estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix
  p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames
  setNames smoothed start tbl_dt term value voom voomWithQualityWeights
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "end", "model.matrix", "p.adjust", "setNames",
             "start")
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 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
DESeq2_tidiers 8.42   0.01    9.15
edgeR_tidiers  7.53   0.05    7.59
MSnSet_tidiers 1.81   0.03    7.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
DESeq2_tidiers 8.96   0.17   11.74
edgeR_tidiers  6.78   0.02    6.80
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/biobroom.Rcheck/00check.log'
for details.


biobroom.Rcheck/00install.out:


install for i386

* installing *source* package 'biobroom' ...
** 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

install for x64

* installing *source* package 'biobroom' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biobroom' as biobroom_1.5.2.zip
* DONE (biobroom)

biobroom.Rcheck/examples_i386/biobroom-Ex.timings:

nameusersystemelapsed
DESeq2_tidiers8.420.019.15
ExpressionSet_tidiers1.420.052.18
GRanges_tidiers000
MSnSet_tidiers1.810.037.78
SummarizedExperiment_tidiers000
edgeR_tidiers7.530.057.59
limma_tidiers0.300.000.29
qvalue_tidiers0.670.003.71

biobroom.Rcheck/examples_x64/biobroom-Ex.timings:

nameusersystemelapsed
DESeq2_tidiers 8.96 0.1711.74
ExpressionSet_tidiers1.520.011.53
GRanges_tidiers000
MSnSet_tidiers1.980.112.51
SummarizedExperiment_tidiers000
edgeR_tidiers6.780.026.80
limma_tidiers0.390.000.39
qvalue_tidiers0.770.000.77