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BioC 3.0: CHECK report for scsR on moscato1

This page was generated on 2015-04-10 09:50:09 -0700 (Fri, 10 Apr 2015).

Package 805/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scsR 1.3.2
Andrea Franceschini , Roger Meier , Christian von Mering
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/scsR
Last Changed Rev: 97848 / Revision: 102249
Last Changed Date: 2014-12-22 07:04:14 -0800 (Mon, 22 Dec 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: scsR
Version: 1.3.2
Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.3.2.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.3.2.tar.gz
StartedAt: 2015-04-10 05:27:49 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:33:40 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 351.3 seconds
RetCode: 0
Status:  OK  
CheckDir: scsR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.3.2.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/scsR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scsR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scsR' version '1.3.2'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'STRINGdb' 'BiocGenerics' 'Biostrings' 'IRanges' 'plyr' 'tcltk'
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 'scsR' 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
enrichment_heatmap: no visible global function definition for
  'heatmap.2'
* 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' ... [56s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 23.26   0.03   23.42
** running examples for arch 'x64' ... [63s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 27.52   0.11   27.63
* 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 were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/scsR.Rcheck/00check.log'
for details.

scsR.Rcheck/00install.out:


install for i386

* installing *source* package 'scsR' ...
** 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 'scsR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scsR' as scsR_1.3.2.zip
* DONE (scsR)

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

nameusersystemelapsed
add_rank_col0.670.000.67
add_seed0.250.020.27
benchmark_shared_hits3.130.033.17
bydf0.440.000.43
check_consistency2.320.062.55
compare_sorted_geneSets23.26 0.0323.42
create_sd_matrix0.360.000.36
delColDf0.250.000.25
delete_undefined_rows0.480.010.50
enrichment_geneSet0.520.020.53
enrichment_heatmap0.450.030.48
get_sd_quant1.090.021.11
get_seed_oligos_df1.010.001.01
intersectAll000
launch_RSA0.660.000.66
median_replicates1.010.011.03
plot_screen_hits2.110.002.10
plot_seeds_methods2.200.003.07
randomSortOnVal0.420.000.42
randomizeInner0.380.020.39
removeSharedOffTargets1.170.011.19
renameColDf0.260.000.26
replace_non_null_elements0.470.000.47
seed_correction0.840.000.84
seed_correction_pooled0.720.000.72
seed_removal0.510.000.52
seeds_analysis1.950.001.95
sortInner0.330.000.32
split_df0.330.000.33
transcribe_seqs0.360.020.38

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

nameusersystemelapsed
add_rank_col0.830.011.01
add_seed0.340.020.36
benchmark_shared_hits4.710.004.72
bydf0.60.00.6
check_consistency3.210.003.21
compare_sorted_geneSets27.52 0.1127.63
create_sd_matrix0.370.000.37
delColDf0.250.000.25
delete_undefined_rows0.530.020.54
enrichment_geneSet0.410.010.43
enrichment_heatmap0.400.020.42
get_sd_quant1.170.001.17
get_seed_oligos_df1.000.021.01
intersectAll000
launch_RSA0.70.00.7
median_replicates0.800.060.86
plot_screen_hits2.130.012.15
plot_seeds_methods2.390.002.39
randomSortOnVal0.300.000.29
randomizeInner0.320.020.35
removeSharedOffTargets1.370.001.37
renameColDf0.270.010.29
replace_non_null_elements0.230.000.23
seed_correction0.550.000.55
seed_correction_pooled0.590.000.59
seed_removal0.550.020.56
seeds_analysis1.90.01.9
sortInner0.300.020.31
split_df0.280.000.29
transcribe_seqs0.370.010.39