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BioC 3.4: CHECK report for iCOBRA on moscato1

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

Package 600/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCOBRA 1.1.2
Charlotte Soneson
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iCOBRA
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: iCOBRA
Version: 1.1.2
Command: rm -rf iCOBRA.buildbin-libdir iCOBRA.Rcheck && mkdir iCOBRA.buildbin-libdir iCOBRA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iCOBRA.buildbin-libdir iCOBRA_1.1.2.tar.gz >iCOBRA.Rcheck\00install.out 2>&1 && cp iCOBRA.Rcheck\00install.out iCOBRA-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=iCOBRA.buildbin-libdir --install="check:iCOBRA-install.out" --force-multiarch --no-vignettes --timings iCOBRA_1.1.2.tar.gz
StartedAt: 2016-09-20 10:30:18 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:33:57 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 218.3 seconds
RetCode: 0
Status:  OK  
CheckDir: iCOBRA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf iCOBRA.buildbin-libdir iCOBRA.Rcheck && mkdir iCOBRA.buildbin-libdir iCOBRA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iCOBRA.buildbin-libdir iCOBRA_1.1.2.tar.gz >iCOBRA.Rcheck\00install.out 2>&1 && cp iCOBRA.Rcheck\00install.out iCOBRA-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=iCOBRA.buildbin-libdir --install="check:iCOBRA-install.out" --force-multiarch --no-vignettes --timings iCOBRA_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/iCOBRA.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 'iCOBRA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iCOBRA' version '1.1.2'
* 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 'iCOBRA' 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 ... OK
* 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 '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: OK

iCOBRA.Rcheck/00install.out:


install for i386

* installing *source* package 'iCOBRA' ...
** 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 'iCOBRA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iCOBRA' as iCOBRA_1.1.2.zip
* DONE (iCOBRA)

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

nameusersystemelapsed
COBRAData0.020.000.01
COBRAPerformance000
COBRAPlot000
COBRAapp0.000.000.17
Extract0.180.020.21
basemethods0.460.010.46
calculate_adjp0.020.000.02
calculate_performance0.930.000.93
coerce0.160.000.16
corr0.030.000.03
deviation0.620.000.62
facetted0.110.000.11
fdrnbr0.110.000.11
fdrnbrcurve0.390.000.39
fdrtpr0.100.000.09
fdrtprcurve0.390.000.39
fpc0.450.000.46
fpr0.080.000.08
maxsplit0.230.020.24
onlyshared0.090.000.10
overlap0.020.000.01
padj0.000.010.02
plot_corr0.300.020.31
plot_deviation1.090.001.19
plot_fdrnbrcurve0.950.010.96
plot_fdrtprcurve0.890.001.58
plot_fpc0.720.000.76
plot_fpr0.340.000.35
plot_overlap0.060.000.07
plot_roc0.770.020.78
plot_scatter1.150.001.16
plot_tpr0.310.000.31
plot_upset1.380.001.37
plotcolors0.090.000.09
prepare_data_for_plot0.920.020.94
pval0.020.000.02
reorder_levels000
roc0.460.000.46
scatter0.640.000.64
score0.020.000.02
splv0.230.000.23
stratiflevels0.330.000.33
tpr0.080.000.08
truth0.020.000.01

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

nameusersystemelapsed
COBRAData0.020.000.01
COBRAPerformance000
COBRAPlot0.010.000.02
COBRAapp000
Extract0.140.010.16
basemethods0.440.000.43
calculate_adjp0.030.000.03
calculate_performance0.980.000.99
coerce0.190.000.18
corr0.030.000.03
deviation0.610.000.61
facetted0.130.000.12
fdrnbr0.100.000.11
fdrnbrcurve0.390.000.39
fdrtpr0.180.000.18
fdrtprcurve0.350.000.35
fpc0.440.010.46
fpr0.160.000.15
maxsplit0.260.000.27
onlyshared0.160.000.15
overlap0.010.000.02
padj0.020.000.01
plot_corr0.360.000.36
plot_deviation1.220.001.22
plot_fdrnbrcurve1.020.021.03
plot_fdrtprcurve1.070.001.34
plot_fpc0.770.021.01
plot_fpr0.510.000.52
plot_overlap0.040.000.05
plot_roc0.800.000.83
plot_scatter1.250.001.43
plot_tpr0.370.000.37
plot_upset1.690.001.69
plotcolors0.110.000.11
prepare_data_for_plot0.950.000.95
pval0.010.000.02
reorder_levels000
roc0.390.000.39
scatter0.600.000.59
score0.010.000.01
splv0.270.000.27
stratiflevels0.370.000.37
tpr0.080.010.10
truth0.010.000.01