Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X [Y] Z 

BioC 3.4: CHECK report for YAPSA on moscato1

This page was generated on 2016-09-21 03:48:49 -0700 (Wed, 21 Sep 2016).

Package 1255/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 0.99.10
Daniel Huebschmann
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/YAPSA
Last Changed Rev: 120522 / Revision: 121152
Last Changed Date: 2016-08-26 12:47:20 -0700 (Fri, 26 Aug 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: YAPSA
Version: 0.99.10
Command: rm -rf YAPSA.buildbin-libdir YAPSA.Rcheck && mkdir YAPSA.buildbin-libdir YAPSA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=YAPSA.buildbin-libdir YAPSA_0.99.10.tar.gz >YAPSA.Rcheck\00install.out 2>&1 && cp YAPSA.Rcheck\00install.out YAPSA-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=YAPSA.buildbin-libdir --install="check:YAPSA-install.out" --force-multiarch --no-vignettes --timings YAPSA_0.99.10.tar.gz
StartedAt: 2016-09-20 18:24:40 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 18:33:37 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 537.0 seconds
RetCode: 0
Status:  OK  
CheckDir: YAPSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf YAPSA.buildbin-libdir YAPSA.Rcheck && mkdir YAPSA.buildbin-libdir YAPSA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=YAPSA.buildbin-libdir YAPSA_0.99.10.tar.gz >YAPSA.Rcheck\00install.out 2>&1 && cp YAPSA.Rcheck\00install.out YAPSA-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=YAPSA.buildbin-libdir --install="check:YAPSA-install.out" --force-multiarch --no-vignettes --timings YAPSA_0.99.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/YAPSA.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 'YAPSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'YAPSA' version '0.99.10'
* 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 'YAPSA' 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
Examples with CPU or elapsed time > 5s
        user system elapsed
run_SMC 6.06   0.17    6.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
run_SMC 5.89   0.19    6.09
* 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

YAPSA.Rcheck/00install.out:


install for i386

* installing *source* package 'YAPSA' ...
** 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 'YAPSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_0.99.10.zip
* DONE (YAPSA)

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

nameusersystemelapsed
LCD0.010.000.02
LCD_complex_cutoff0.020.000.02
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.040.000.03
annotate_intermut_dist_cohort0.040.000.05
annotation_exposures_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges000
build_gene_list_for_pathway000
compare_SMCs0.020.000.02
compare_exposures000
compare_sets000
compare_to_catalogues000
complex_heatmap_exposures0.870.000.87
compute_comparison_stat_df000
cosineDist000
create_mutation_catalogue_from_VR2.150.112.26
create_mutation_catalogue_from_df1.000.081.08
cut_breaks_as_intervals0.240.000.23
exampleYAPSA0.100.010.11
exposures_barplot0.850.000.85
extract_names_from_gene_list000
find_affected_PIDs000
get_extreme_PIDs0.050.000.05
hclust_exposures0.010.000.01
makeVRangesFromDataFrame0.130.000.13
make_catalogue_strata_df000
make_comparison_matrix0.140.000.14
make_strata_df000
make_subgroups_df0.080.000.06
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.020.000.02
plotExchangeSpectra000
plot_SMC000
plot_exposures0.730.000.74
plot_strata000
repeat_df0.020.000.01
run_SMC6.060.176.26
run_annotate_vcf_pl000
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible0.000.000.03
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC000
stat_test_subgroups000
stderrmean0.000.000.01
sum_over_list_of_df000
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg190.010.000.02
trellis_rainfall_plot3.390.003.54

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

nameusersystemelapsed
LCD0.020.000.01
LCD_complex_cutoff000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.030.000.03
annotate_intermut_dist_cohort0.050.000.04
annotation_exposures_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges0.010.000.02
build_gene_list_for_pathway000
compare_SMCs000
compare_exposures000
compare_sets000
compare_to_catalogues000
complex_heatmap_exposures0.950.000.95
compute_comparison_stat_df000
cosineDist000
create_mutation_catalogue_from_VR2.490.062.56
create_mutation_catalogue_from_df1.110.111.22
cut_breaks_as_intervals0.230.000.24
exampleYAPSA0.090.000.10
exposures_barplot0.920.000.92
extract_names_from_gene_list000
find_affected_PIDs000
get_extreme_PIDs0.040.000.05
hclust_exposures000
makeVRangesFromDataFrame0.130.000.12
make_catalogue_strata_df000
make_comparison_matrix0.150.000.16
make_strata_df000
make_subgroups_df0.050.030.08
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.020.000.01
plotExchangeSpectra000
plot_SMC000
plot_exposures0.780.000.78
plot_strata000
repeat_df000
run_SMC5.890.196.09
run_annotate_vcf_pl0.020.000.01
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible0.000.000.02
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC0.010.000.01
stat_test_subgroups000
stderrmean000
sum_over_list_of_df000
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg190.020.000.02
trellis_rainfall_plot4.010.004.01