Andrea Franceschini
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/scsR |
| Branch: RELEASE_3_9 |
| Last Commit: f7d9689 |
| Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:29:18 -0400 (Wed, 16 Oct 2019).
| Package 1480/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scsR 1.20.0 Andrea Franceschini
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: scsR |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scsR_1.20.0.tar.gz |
| StartedAt: 2019-10-16 06:58:29 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:02:07 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 218.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scsR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scsR_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/scsR.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '1.20.0' * 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 * 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 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 OPIrsaScore :: no visible global function definition for 'phyper' enrichment_geneSet: no visible global function definition for 'phyper' enrichment_heatmap: no visible global function definition for 'heatmap.2' get_seed_oligos_df: no visible global function definition for 'txtProgressBar' get_seed_oligos_df: no visible global function definition for 'setTxtProgressBar' get_seed_oligos_df: no visible global function definition for 'phyper' get_seed_oligos_df: no visible global function definition for 'ks.test' plot_seed_score_sd: no visible global function definition for 'lm' plot_seed_score_sd: no visible global function definition for 'cor.test' seed_correction: no visible global function definition for 'txtProgressBar' seed_correction: no visible global function definition for 'setTxtProgressBar' seed_correction_pooled: no visible global function definition for 'txtProgressBar' seed_correction_pooled: no visible global function definition for 'setTxtProgressBar' seed_removal: no visible global function definition for 'txtProgressBar' seed_removal: no visible global function definition for 'setTxtProgressBar' seeds_analysis : : no visible global function definition for 'ks.test' seeds_analysis: no visible global function definition for 'phyper' transcribe_seqs: no visible global function definition for 'txtProgressBar' transcribe_seqs: no visible global function definition for 'setTxtProgressBar' Undefined global functions or variables: cor.test heatmap.2 ks.test lm phyper setTxtProgressBar txtProgressBar Consider adding importFrom("stats", "cor.test", "ks.test", "lm", "phyper") importFrom("utils", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed compare_sorted_geneSets 13.32 0.19 13.5 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed compare_sorted_geneSets 16.52 0.14 16.65 * 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:/Users/biocbuild/bbs-3.9-bioc/meat/scsR.Rcheck/00check.log' for details.
scsR.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/scsR_1.20.0.tar.gz && rm -rf scsR.buildbin-libdir && mkdir scsR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scsR.buildbin-libdir scsR_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL scsR_1.20.0.zip && rm scsR_1.20.0.tar.gz scsR_1.20.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1790k 100 1790k 0 0 23.5M 0 --:--:-- --:--:-- --:--:-- 26.1M
install for i386
* installing *source* package 'scsR' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scsR'
finding HTML links ... done
OPIrsa html
OPIrsaScore html
add_rank_col html
add_seed html
benchmark_shared_hits html
bydf html
check_consistency html
compare_sorted_geneSets html
create_sd_matrix html
delColDf html
delete_undefined_rows html
enrichment_geneSet html
enrichment_heatmap html
get_sd_quant html
get_seed_oligos_df html
intersectAll html
launch_RSA html
median_replicates html
miRBase_20 html
plot_screen_hits html
plot_seeds_methods html
randomSortOnVal html
randomizeInner html
removeSharedOffTargets html
renameColDf html
replace_non_null_elements html
seed_correction html
seed_correction_pooled html
seed_removal html
seeds_analysis html
sortInner html
split_df html
transcribe_seqs html
uuk_screen html
uuk_screen_dh html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'scsR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scsR' as scsR_1.20.0.zip
* DONE (scsR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'scsR' successfully unpacked and MD5 sums checked
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scsR.Rcheck/examples_i386/scsR-Ex.timings
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scsR.Rcheck/examples_x64/scsR-Ex.timings
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