BioC 3.2: CHECK report for scsR on windows1.bioconductor.org
This page was generated on 2015-10-27 17:31:04 -0400 (Tue, 27 Oct 2015).
scsR 1.6.0 Andrea Franceschini , Roger Meier , Christian von Mering
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/scsR | Last Changed Rev: 109589 / Revision: 109947 | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
windows1.bioconductor.org | Windows Server 2012 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
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Version: 1.6.0
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Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.6.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.6.0.tar.gz
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StartedAt: 2015-10-27 05:28:12 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 05:31:33 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 200.8 seconds
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RetCode: 0
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Status: OK
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CheckDir: scsR.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.6.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.6.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/scsR.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-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 '1.6.0'
* 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' ... [35s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
compare_sorted_geneSets 13.2 0.19 13.39
** running examples for arch 'x64' ... [41s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
compare_sorted_geneSets 17.28 0.17 17.49
* 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: 2 NOTEs
See
'C:/biocbld/bbs-3.2-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_1.6.0.zip
* DONE (scsR)
scsR.Rcheck/examples_i386/scsR-Ex.timings:
name | user | system | elapsed
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add_rank_col | 0.3 | 0.0 | 0.3 |
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add_seed | 0.23 | 0.00 | 0.24 |
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benchmark_shared_hits | 2.33 | 0.03 | 2.35 |
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bydf | 0.33 | 0.00 | 0.33 |
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check_consistency | 1.63 | 0.06 | 1.69 |
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compare_sorted_geneSets | 13.20 | 0.19 | 13.39 |
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create_sd_matrix | 0.44 | 0.00 | 0.44 |
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delColDf | 0.18 | 0.00 | 0.19 |
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delete_undefined_rows | 0.42 | 0.00 | 0.42 |
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enrichment_geneSet | 0.41 | 0.00 | 0.41 |
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enrichment_heatmap | 0.37 | 0.02 | 0.39 |
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get_sd_quant | 0.83 | 0.01 | 0.84 |
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get_seed_oligos_df | 0.64 | 0.00 | 0.64 |
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intersectAll | 0 | 0 | 0 |
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launch_RSA | 0.36 | 0.00 | 0.36 |
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median_replicates | 0.77 | 0.02 | 0.79 |
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plot_screen_hits | 1.32 | 0.01 | 1.34 |
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plot_seeds_methods | 1.44 | 0.00 | 1.44 |
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randomSortOnVal | 0.16 | 0.07 | 0.22 |
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randomizeInner | 0.22 | 0.00 | 0.21 |
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removeSharedOffTargets | 0.70 | 0.00 | 0.71 |
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renameColDf | 0.22 | 0.00 | 0.22 |
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replace_non_null_elements | 0.22 | 0.00 | 0.21 |
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seed_correction | 0.48 | 0.01 | 0.50 |
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seed_correction_pooled | 0.39 | 0.00 | 0.40 |
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seed_removal | 0.35 | 0.00 | 0.34 |
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seeds_analysis | 1.31 | 0.00 | 1.31 |
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sortInner | 0.26 | 0.00 | 0.27 |
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split_df | 0.25 | 0.00 | 0.25 |
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transcribe_seqs | 0.29 | 0.02 | 0.29 |
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scsR.Rcheck/examples_x64/scsR-Ex.timings:
name | user | system | elapsed
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add_rank_col | 0.31 | 0.00 | 0.31 |
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add_seed | 0.5 | 0.0 | 0.5 |
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benchmark_shared_hits | 2.61 | 0.01 | 2.62 |
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bydf | 0.38 | 0.03 | 0.41 |
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check_consistency | 1.7 | 0.0 | 1.7 |
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compare_sorted_geneSets | 17.28 | 0.17 | 17.49 |
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create_sd_matrix | 0.35 | 0.02 | 0.36 |
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delColDf | 0.2 | 0.0 | 0.2 |
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delete_undefined_rows | 0.39 | 0.02 | 0.41 |
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enrichment_geneSet | 0.38 | 0.03 | 0.40 |
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enrichment_heatmap | 0.40 | 0.01 | 0.42 |
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get_sd_quant | 0.99 | 0.02 | 1.00 |
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get_seed_oligos_df | 0.70 | 0.01 | 0.72 |
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intersectAll | 0 | 0 | 0 |
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launch_RSA | 0.37 | 0.00 | 0.38 |
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median_replicates | 0.71 | 0.02 | 0.72 |
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plot_screen_hits | 1.42 | 0.00 | 1.42 |
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plot_seeds_methods | 1.73 | 0.02 | 1.76 |
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randomSortOnVal | 0.21 | 0.01 | 0.22 |
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randomizeInner | 0.18 | 0.00 | 0.19 |
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removeSharedOffTargets | 1 | 0 | 1 |
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renameColDf | 0.19 | 0.02 | 0.20 |
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replace_non_null_elements | 0.19 | 0.00 | 0.19 |
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seed_correction | 0.45 | 0.00 | 0.45 |
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seed_correction_pooled | 0.52 | 0.01 | 0.54 |
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seed_removal | 0.36 | 0.00 | 0.36 |
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seeds_analysis | 1.56 | 0.02 | 1.57 |
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sortInner | 0.23 | 0.00 | 0.24 |
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split_df | 0.21 | 0.01 | 0.22 |
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transcribe_seqs | 0.25 | 0.00 | 0.25 |
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