Andrea Franceschini
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/scsR |
| Branch: RELEASE_3_8 |
| Last Commit: 1a01bfa |
| Last Changed Date: 2018-10-30 11:41:53 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:23:35 -0400 (Sat, 13 Apr 2019).
| Package 1407/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scsR 1.18.0 Andrea Franceschini
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: scsR |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings scsR_1.18.0.tar.gz |
| StartedAt: 2019-04-13 05:22:13 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:26:27 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 253.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scsR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings scsR_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/scsR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 : <anonymous>: 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 : <anonymous>: 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 16.05 0.15 16.2
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compare_sorted_geneSets 17.36 0.14 17.5
* 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-3.8-bioc/meat/scsR.Rcheck/00check.log'
for details.
scsR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/scsR_1.18.0.tar.gz && rm -rf scsR.buildbin-libdir && mkdir scsR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scsR.buildbin-libdir scsR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL scsR_1.18.0.zip && rm scsR_1.18.0.tar.gz scsR_1.18.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 1791k 100 1791k 0 0 31.1M 0 --:--:-- --:--:-- --:--:-- 32.4M
install for i386
* installing *source* package 'scsR' ...
** 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
In R CMD INSTALL
install for x64
* installing *source* package 'scsR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scsR' as scsR_1.18.0.zip
* DONE (scsR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'scsR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
scsR.Rcheck/examples_i386/scsR-Ex.timings
|
scsR.Rcheck/examples_x64/scsR-Ex.timings
|