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BioC 3.5: CHECK report for Metab on tokay2

This page was generated on 2017-08-16 13:24:00 -0400 (Wed, 16 Aug 2017).

Package 786/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Metab 1.10.0
Raphael Aggio
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Metab
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
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
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Metab
Version: 1.10.0
Command: rm -rf Metab.buildbin-libdir Metab.Rcheck && mkdir Metab.buildbin-libdir Metab.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Metab.buildbin-libdir Metab_1.10.0.tar.gz >Metab.Rcheck\00install.out 2>&1 && cp Metab.Rcheck\00install.out Metab-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Metab.buildbin-libdir --install="check:Metab-install.out" --force-multiarch --no-vignettes --timings Metab_1.10.0.tar.gz
StartedAt: 2017-08-16 01:05:09 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:09:43 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 273.9 seconds
RetCode: 0
Status:  OK  
CheckDir: Metab.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Metab.buildbin-libdir Metab.Rcheck && mkdir Metab.buildbin-libdir Metab.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Metab.buildbin-libdir Metab_1.10.0.tar.gz >Metab.Rcheck\00install.out 2>&1 && cp Metab.Rcheck\00install.out Metab-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Metab.buildbin-libdir --install="check:Metab-install.out" --force-multiarch --no-vignettes --timings Metab_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Metab.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 'Metab/DESCRIPTION' ... OK
* this is package 'Metab' version '1.10.0'
* 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 'Metab' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
MetReport: no visible global function definition for 'read.csv'
MetReport: no visible global function definition for 'write.csv'
MetReportNames: no visible global function definition for 'read.csv'
MetReportNames: no visible global function definition for 'write.csv'
buildLib: no visible global function definition for 'read.csv'
buildLib: no visible global function definition for 'txtProgressBar'
buildLib: no visible global function definition for 'setTxtProgressBar'
buildLib: no visible global function definition for 'write.csv'
htest : test.t : <anonymous>: no visible global function definition for
  't.test'
htest : anova.t : <anonymous>: no visible global function definition
  for 'lm'
htest : anova.t: no visible binding for global variable 'anova'
htest: no visible global function definition for 'read.csv'
htest: no visible global function definition for 'p.adjust'
htest: no visible global function definition for 'write.csv'
normalizeByBiomass: no visible global function definition for
  'read.csv'
normalizeByBiomass: no visible global function definition for
  'write.csv'
normalizeByInternalStandard: no visible global function definition for
  'read.csv'
normalizeByInternalStandard: no visible global function definition for
  'select.list'
normalizeByInternalStandard: no visible global function definition for
  'write.csv'
removeFalsePositives: no visible global function definition for
  'read.csv'
removeFalsePositives: no visible global function definition for
  'write.csv'
Undefined global functions or variables:
  anova lm p.adjust read.csv select.list setTxtProgressBar t.test
  txtProgressBar write.csv
Consider adding
  importFrom("stats", "anova", "lm", "p.adjust", "t.test")
  importFrom("utils", "read.csv", "select.list", "setTxtProgressBar",
             "txtProgressBar", "write.csv")
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
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/Metab.Rcheck/00check.log'
for details.


Metab.Rcheck/00install.out:


install for i386

* installing *source* package 'Metab' ...
** 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 'Metab' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Metab' as Metab_1.10.0.zip
* DONE (Metab)

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

nameusersystemelapsed
MetReport0.170.040.28
MetReportNames0.360.030.39
Metab-package0.010.000.01
buildLib0.700.000.77
exampleAMDISReport0.050.020.07
exampleBiomass000
exampleHtest0.000.010.02
exampleIonLib0.000.020.01
exampleMSLfile0.000.030.03
exampleMetReport000
htest0.310.020.33
normalizeByBiomass0.010.020.03
normalizeByInternalStandard0.020.000.01
removeFalsePositives0.020.000.02

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

nameusersystemelapsed
MetReport0.160.030.24
MetReportNames0.480.000.48
Metab-package0.010.000.01
buildLib0.650.020.74
exampleAMDISReport0.030.030.06
exampleBiomass0.000.010.02
exampleHtest000
exampleIonLib000
exampleMSLfile000
exampleMetReport000
htest0.360.020.38
normalizeByBiomass0.020.020.03
normalizeByInternalStandard0.010.000.01
removeFalsePositives0.040.000.04