Pumin Li
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/primirTSS |
| Branch: RELEASE_3_8 |
| Last Commit: 3be26c7 |
| Last Changed Date: 2019-01-04 13:45:03 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:39 -0400 (Sat, 13 Apr 2019).
| Package 1189/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| primirTSS 1.0.1 Pumin Li
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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: primirTSS |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:primirTSS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings primirTSS_1.0.1.tar.gz |
| StartedAt: 2019-04-13 04:40:02 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:46:11 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 368.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: primirTSS.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:primirTSS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings primirTSS_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/primirTSS.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 'primirTSS/DESCRIPTION' ... OK * this is package 'primirTSS' version '1.0.1' * package encoding: UTF-8 * 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' 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 'primirTSS' 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 check_DHS_df: no visible binding for global variable 'can_tss' check_DHS_df: no visible binding for global variable 'new_info' check_DHS_s: no visible binding for global variable 'dhs_p1' check_DHS_s: no visible binding for global variable 'dhs_p2' eponine_score: no visible binding for global variable 'previous' eponine_score: no visible binding for global variable 'histone_p1_flank' eponine_score: no visible binding for global variable 'histone_p2_flank' eponine_score: no visible binding for global variable 'tss_p1' eponine_score: no visible binding for global variable 'tss_p2' find_nearest_peak: no visible binding for global variable 'mir_name' find_nearest_peak: no visible binding for global variable 'start1' find_nearest_peak: no visible binding for global variable 'end1' mir_tf: no visible binding for global variable 'arrow' mir_tf: no visible binding for global variable 'seqname' mir_tf: no visible binding for global variable 'TF' mir_tf: no visible binding for global variable 'TF_class' phast_score: no visible binding for global variable 'loci' phast_score: no visible binding for global variable 'eponine_rank' phast_score: no visible binding for global variable 'phast_rank' phast_score: no visible binding for global variable 'e_p_rank' phast_score_plot: no visible binding for global variable 'loci' plot_primiRNA_track: no visible binding for global variable 'predicted_tss' plot_primiRNA_track: no visible binding for global variable 'symbol_name' plot_primiRNA_track: no visible binding for global variable 'stem_loop_p1' plot_primiRNA_track: no visible binding for global variable 'stem_loop_p2' plot_primiRNA_track: no visible binding for global variable 'gene_id' plot_primiRNA_track: no visible binding for global variable 'gene_p1' plot_primiRNA_track: no visible binding for global variable 'gene_p2' plot_primiRNA_track: no visible binding for global variable 'tss_p1' plot_primiRNA_track: no visible binding for global variable 'tss_p2' require_fa: no visible binding for global variable 'arrow' tss_filter: no visible binding for global variable 'gene_id' tss_filter: no visible binding for global variable 'new_info' tss_filter: no visible binding for global variable 'predicted_tss' tss_filter: no visible binding for global variable 'tss_type' Undefined global functions or variables: TF TF_class arrow can_tss dhs_p1 dhs_p2 e_p_rank end1 eponine_rank gene_id gene_p1 gene_p2 histone_p1_flank histone_p2_flank loci mir_name new_info phast_rank predicted_tss previous seqname start1 stem_loop_p1 stem_loop_p2 symbol_name tss_p1 tss_p2 tss_type * 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 R/sysdata.rda ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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: 1 NOTE See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/primirTSS.Rcheck/00check.log' for details.
primirTSS.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/primirTSS_1.0.1.tar.gz && rm -rf primirTSS.buildbin-libdir && mkdir primirTSS.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=primirTSS.buildbin-libdir primirTSS_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL primirTSS_1.0.1.zip && rm primirTSS_1.0.1.tar.gz primirTSS_1.0.1.zip
###
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install for i386
* installing *source* package 'primirTSS' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'primirTSS'
finding HTML links ... done
find_tss html
peak_join html
peak_merge html
plot_primiRNA html
primirTSS html
run_primirTSSapp html
trans_cor html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'primirTSS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'primirTSS' as primirTSS_1.0.1.zip
* DONE (primirTSS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'primirTSS' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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primirTSS.Rcheck/examples_i386/primirTSS-Ex.timings
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primirTSS.Rcheck/examples_x64/primirTSS-Ex.timings
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