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BioC experimental data: CHECK report for SomaticCancerAlterations on moscato1

This page was generated on 2016-05-28 20:31:17 -0700 (Sat, 28 May 2016).

Package 262/292HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SomaticCancerAlterations 1.9.2
Julian Gehring
Snapshot Date: 2016-05-28 09:20:19 -0700 (Sat, 28 May 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/SomaticCancerAlterations
Last Changed Rev: 3773 / Revision: 3781
Last Changed Date: 2016-05-15 13:21:08 -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 

Summary

Package: SomaticCancerAlterations
Version: 1.9.2
Command: rm -rf SomaticCancerAlterations.buildbin-libdir SomaticCancerAlterations.Rcheck && mkdir SomaticCancerAlterations.buildbin-libdir SomaticCancerAlterations.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SomaticCancerAlterations.buildbin-libdir SomaticCancerAlterations_1.9.2.tar.gz >SomaticCancerAlterations.Rcheck\00install.out 2>&1 && cp SomaticCancerAlterations.Rcheck\00install.out SomaticCancerAlterations-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SomaticCancerAlterations.buildbin-libdir --install="check:SomaticCancerAlterations-install.out" --force-multiarch --no-vignettes --timings SomaticCancerAlterations_1.9.2.tar.gz
StartedAt: 2016-05-28 16:51:34 -0700 (Sat, 28 May 2016)
EndedAt: 2016-05-28 17:02:04 -0700 (Sat, 28 May 2016)
EllapsedTime: 629.7 seconds
RetCode: 0
Status:  OK  
CheckDir: SomaticCancerAlterations.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   rm -rf SomaticCancerAlterations.buildbin-libdir SomaticCancerAlterations.Rcheck && mkdir SomaticCancerAlterations.buildbin-libdir SomaticCancerAlterations.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SomaticCancerAlterations.buildbin-libdir SomaticCancerAlterations_1.9.2.tar.gz >SomaticCancerAlterations.Rcheck\00install.out 2>&1 && cp SomaticCancerAlterations.Rcheck\00install.out SomaticCancerAlterations-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SomaticCancerAlterations.buildbin-libdir --install="check:SomaticCancerAlterations-install.out" --force-multiarch --no-vignettes --timings SomaticCancerAlterations_1.9.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-data-experiment/meat/SomaticCancerAlterations.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SomaticCancerAlterations/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SomaticCancerAlterations' version '1.9.2'
* package encoding: UTF-8
* 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 'SomaticCancerAlterations' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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 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
.load_dataset: no visible global function definition for 'data'
.maf2gr: no visible binding for global variable 'Chromosome'
.maf2gr: no visible binding for global variable 'Start_position'
.maf2gr: no visible binding for global variable 'End_position'
.read_maf: no visible global function definition for 'read.delim'
hg2ncbi: no visible global function definition for 'seqnameStyle<-'
hg2ncbi: no visible global function definition for 'genome<-'
mutationDensity: no visible global function definition for
  'keepSeqlevels'
ncbi2hg: no visible global function definition for 'seqnameStyle<-'
ncbi2hg: no visible global function definition for 'genome<-'
scaListDatasets: no visible global function definition for 'data'
Undefined global functions or variables:
  Chromosome End_position Start_position data genome<- keepSeqlevels
  read.delim seqnameStyle<-
Consider adding
  importFrom("utils", "data", "read.delim")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
all-functions 0.42      0    6.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test_all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test_all.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-data-experiment/meat/SomaticCancerAlterations.Rcheck/00check.log'
for details.


SomaticCancerAlterations.Rcheck/00install.out:


install for i386

* installing *source* package 'SomaticCancerAlterations' ...
** R
** data
** 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 'SomaticCancerAlterations' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SomaticCancerAlterations' as SomaticCancerAlterations_1.9.2.zip
* DONE (SomaticCancerAlterations)

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

nameusersystemelapsed
all-data0.040.000.05
all-functions0.240.013.69

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

nameusersystemelapsed
all-data0.050.000.05
all-functions0.420.006.04