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BioC 3.0: CHECK report for flowPhyto on moscato1

This page was generated on 2015-02-08 09:46:19 -0800 (Sun, 08 Feb 2015).

Package 316/935HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowPhyto 1.18.0
Chris Berthiaume
Snapshot Date: 2015-02-07 16:20:12 -0800 (Sat, 07 Feb 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/flowPhyto
Last Changed Rev: 95439 / Revision: 99197
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: flowPhyto
Version: 1.18.0
Command: rm -rf flowPhyto.buildbin-libdir flowPhyto.Rcheck && mkdir flowPhyto.buildbin-libdir flowPhyto.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowPhyto.buildbin-libdir flowPhyto_1.18.0.tar.gz >flowPhyto.Rcheck\00install.out 2>&1 && cp flowPhyto.Rcheck\00install.out flowPhyto-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=flowPhyto.buildbin-libdir --install="check:flowPhyto-install.out" --force-multiarch --no-vignettes --timings flowPhyto_1.18.0.tar.gz
StartedAt: 2015-02-08 01:26:20 -0800 (Sun, 08 Feb 2015)
EndedAt: 2015-02-08 01:32:12 -0800 (Sun, 08 Feb 2015)
EllapsedTime: 351.7 seconds
RetCode: 0
Status:  OK  
CheckDir: flowPhyto.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowPhyto.buildbin-libdir flowPhyto.Rcheck && mkdir flowPhyto.buildbin-libdir flowPhyto.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowPhyto.buildbin-libdir flowPhyto_1.18.0.tar.gz >flowPhyto.Rcheck\00install.out 2>&1 && cp flowPhyto.Rcheck\00install.out flowPhyto-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=flowPhyto.buildbin-libdir --install="check:flowPhyto-install.out" --force-multiarch --no-vignettes --timings flowPhyto_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/flowPhyto.Rcheck'
* using R version 3.1.2 (2014-10-31)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowPhyto/DESCRIPTION' ... OK
* this is package 'flowPhyto' version '1.18.0'
* 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 'flowPhyto' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.DBcon: no visible global function definition for 'dbConnect'
.DBcon: no visible global function definition for 'dbDriver'
.DBcon: no visible binding for global variable '.db.driver'
.DBcon: no visible binding for global variable '.db.user'
.DBcon: no visible binding for global variable '.db.pass'
.DBcon: no visible binding for global variable '.db.name'
.DBcon: no visible binding for global variable '.db.host'
.interpolateSDSLatLon: no visible global function definition for
  'na.approx'
.loadSDS: no visible global function definition for 'dbReadTable'
.loadSDS: no visible binding for global variable '.db.cruise.tab.nm'
.loadSDS: no visible global function definition for 'dbGetQuery'
.loadSDS: no visible binding for global variable '.db.sds.tab.nm'
.loadSDS: no visible binding for global variable '.db.cruise.fkey.nm'
.loadSDS: no visible global function definition for 'dbListFields'
.loadSDS: no visible global function definition for 'dbWriteTable'
.loadStats: no visible global function definition for 'dbReadTable'
.loadStats: no visible binding for global variable '.db.cruise.tab.nm'
.loadStats: no visible global function definition for 'dbGetQuery'
.loadStats: no visible binding for global variable '.db.stats.tab.nm'
.loadStats: no visible binding for global variable '.db.cruise.fkey.nm'
.loadStats: no visible global function definition for 'dbListFields'
.loadStats: no visible global function definition for 'dbWriteTable'
.prePlotLevel2: no visible binding for global variable '.SOURCE.DIR'
.queryStats: no visible binding for global variable '.db.stats.tab.nm'
.queryStats: no visible binding for global variable
  '.db.cruise.fkey.nm'
.queryStats: no visible binding for global variable '.db.cruise.tab.nm'
classify: no visible binding for global variable 'pe'
classify: no visible binding for global variable 'chl_small'
classify: no visible binding for global variable 'fsc_perp'
classify: no visible binding for global variable 'fsc_small'
classify: no visible binding for global variable 'chl_big'
classify: no visible binding for global variable 'pop'
filter: no visible binding for global variable 'D1'
filter: no visible binding for global variable 'D2'
filter: no visible binding for global variable 'fsc_small'
plotCruiseStats: no visible binding for global variable 'resamp'
plotCytogram: no visible binding for global variable 'pop'
plotLatLongMap: no visible global function definition for
  'color.legend'
summarize: no visible binding for global variable 'pop'
summarizeFile: no visible binding for global variable 'pop'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [108s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotCruiseStats 10.26   0.33   10.92
censusFile       4.44   0.15   11.43
pipeline         0.10   0.05   25.04
writeSeaflow     0.06   0.00   30.06
** running examples for arch 'x64' ... [111s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotCruiseStats 7.12   0.38    7.83
census          3.04   0.85    5.73
censusFile      3.71   0.13    9.09
writeSeaflow    0.08   0.00   30.08
pipeline        0.05   0.01   29.30
* 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-bioc/meat/flowPhyto.Rcheck/00check.log'
for details.

flowPhyto.Rcheck/00install.out:


install for i386

* installing *source* package 'flowPhyto' ...
** R
** 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 'flowPhyto' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowPhyto' as flowPhyto_1.18.0.zip
* DONE (flowPhyto)

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

nameusersystemelapsed
CHANNEL.CLMNS000
CHANNEL.CLMNS.SM000
EVT.HEADERS000
POP.DEF0.010.000.02
REPO.PATH000
census3.120.393.51
censusFile 4.44 0.1511.43
classify2.540.543.11
classifyFile0.700.081.32
cleanupLogs000
clearOutputs0.000.001.15
cmdArgsToVariables000
combineCensusFiles0.010.000.02
combineSdsFiles0.020.000.02
consensus1.350.011.37
consensusFile1.130.001.54
createResamplingScheme0.010.000.02
filter0.080.000.08
filterFile1.980.113.30
getCruiseFiles000
getCruisePath0.020.000.02
getFileNumber000
joinSDS0.150.000.15
pipeline 0.10 0.0525.04
plotCruiseStats10.26 0.3310.92
plotCytogram2.950.343.29
plotLatLongMap1.70.11.8
plotStatMap1.530.031.56
readConsensusFile0.020.000.01
readPopDef0.010.000.02
readSeaflow0.090.000.09
summarize0.970.000.97
summarizeFile0.980.012.61
validatePopDef000
writeSeaflow 0.06 0.0030.06

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

nameusersystemelapsed
CHANNEL.CLMNS000
CHANNEL.CLMNS.SM000
EVT.HEADERS000
POP.DEF000
REPO.PATH000
census3.040.855.73
censusFile3.710.139.09
classify2.320.482.81
classifyFile0.750.003.52
cleanupLogs000
clearOutputs0.000.030.87
cmdArgsToVariables000
combineCensusFiles0.020.000.02
combineSdsFiles0.030.000.03
consensus1.650.001.66
consensusFile1.610.023.86
createResamplingScheme0.010.000.02
filter0.100.000.09
filterFile1.650.083.31
getCruiseFiles000
getCruisePath0.010.000.01
getFileNumber000
joinSDS0.170.000.17
pipeline 0.05 0.0129.30
plotCruiseStats7.120.387.83
plotCytogram2.270.402.66
plotLatLongMap1.170.031.21
plotStatMap1.420.081.49
readConsensusFile0.020.000.01
readPopDef0.010.000.02
readSeaflow0.070.000.06
summarize1.230.031.27
summarizeFile0.920.021.85
validatePopDef0.010.000.02
writeSeaflow 0.08 0.0030.08