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BioC 3.5: CHECK report for cellHTS2 on tokay2

This page was generated on 2017-08-16 13:19:41 -0400 (Wed, 16 Aug 2017).

Package 184/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellHTS2 2.40.0
Joseph Barry
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/cellHTS2
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  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellHTS2
Version: 2.40.0
Command: rm -rf cellHTS2.buildbin-libdir cellHTS2.Rcheck && mkdir cellHTS2.buildbin-libdir cellHTS2.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS2.buildbin-libdir cellHTS2_2.40.0.tar.gz >cellHTS2.Rcheck\00install.out 2>&1 && cp cellHTS2.Rcheck\00install.out cellHTS2-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cellHTS2.buildbin-libdir --install="check:cellHTS2-install.out" --force-multiarch --no-vignettes --timings cellHTS2_2.40.0.tar.gz
StartedAt: 2017-08-15 22:33:22 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:40:06 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 403.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cellHTS2.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cellHTS2.buildbin-libdir cellHTS2.Rcheck && mkdir cellHTS2.buildbin-libdir cellHTS2.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS2.buildbin-libdir cellHTS2_2.40.0.tar.gz >cellHTS2.Rcheck\00install.out 2>&1 && cp cellHTS2.Rcheck\00install.out cellHTS2-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cellHTS2.buildbin-libdir --install="check:cellHTS2-install.out" --force-multiarch --no-vignettes --timings cellHTS2_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/cellHTS2.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 'cellHTS2/DESCRIPTION' ... OK
* this is package 'cellHTS2' version '2.40.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'RColorBrewer' 'Biobase' 'genefilter' 'splots' 'vsn' 'hwriter'
  'locfit' 'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'cellHTS2' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    KcViab   2.0Mb
    doc      1.6Mb
* 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
* 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 ... NOTE
Package in Depends field not imported from: 'genefilter'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'Biobase:::.showAnnotatedDataFrame'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Unknown package 'cellHTS' in Rd xrefs
* 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.R'
 OK
** running tests for arch 'x64' ...
  Running 'test.R'
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'GO.db' 'KEGG.db'
* 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 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/cellHTS2.Rcheck/00check.log'
for details.


cellHTS2.Rcheck/00install.out:


install for i386

* installing *source* package 'cellHTS2' ...
** 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 'cellHTS2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellHTS2' as cellHTS2_2.40.0.zip
* DONE (cellHTS2)

cellHTS2.Rcheck/examples_i386/cellHTS2-Ex.timings:

nameusersystemelapsed
Bscore2.200.032.23
ROC-class0.180.000.17
ROC0.780.000.79
annotate0.620.000.62
bdgpbiomart0.210.000.20
buildCellHTS20.380.000.37
cellHTS-class1.180.001.19
configurationAsScreenPlot1.740.001.74
configure0.610.020.62
convertOldCellHTS0.540.000.55
convertWellCoordinates000
data-KcViab0.160.000.15
data-KcViabSmall0.010.000.02
data-dualCh0.020.000.01
data-oldKcViabSmall0.010.000.02
getDynamicRange0.860.010.87
getEnVisionRawData0.070.000.06
getMeasureRepAgreement0.340.040.38
getTopTable0.810.010.83
getZfactor0.270.020.28
imageScreen0.650.000.66
normalizePlates0.820.000.81
oneRowPerId000
plotSpatialEffects1.270.001.27
readHTAnalystData0.530.000.53
readPlateList0.330.000.33
rsa0.60.00.6
scoreReplicates0.530.040.58
scores2calls0.780.000.78
setSettings000
spatialNormalization1.510.001.51
summarizeChannels1.270.001.27
summarizeReplicates0.590.000.59
templateDescriptionFile0.020.000.02
updateCellHTS0.060.000.06
write.tabdel0.050.000.05
writeReport0.000.020.01
writeTab0.010.020.03

cellHTS2.Rcheck/examples_x64/cellHTS2-Ex.timings:

nameusersystemelapsed
Bscore2.890.002.89
ROC-class0.20.00.2
ROC1.380.001.37
annotate0.920.000.92
bdgpbiomart0.200.020.22
buildCellHTS20.50.00.5
cellHTS-class1.140.081.22
configurationAsScreenPlot2.080.012.09
configure0.750.000.75
convertOldCellHTS0.690.000.69
convertWellCoordinates000
data-KcViab0.140.020.16
data-KcViabSmall0.010.000.01
data-dualCh0.020.000.02
data-oldKcViabSmall0.000.020.02
getDynamicRange0.690.000.68
getEnVisionRawData0.050.010.06
getMeasureRepAgreement0.480.000.49
getTopTable1.240.001.23
getZfactor0.450.000.45
imageScreen0.970.000.97
normalizePlates1.280.001.28
oneRowPerId000
plotSpatialEffects2.140.022.16
readHTAnalystData0.730.000.73
readPlateList0.640.000.69
rsa0.940.010.96
scoreReplicates0.780.000.78
scores2calls1.420.021.43
setSettings000
spatialNormalization1.940.001.94
summarizeChannels1.640.001.64
summarizeReplicates0.840.000.84
templateDescriptionFile000
updateCellHTS0.080.000.08
write.tabdel0.060.000.06
writeReport0.020.000.02
writeTab0.030.000.03