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CHECK report for primirTSS on tokay2

This page was generated on 2020-10-17 11:57:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE primirTSS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1348/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
primirTSS 1.6.1
Pumin Li
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/primirTSS
Branch: RELEASE_3_11
Last Commit: e032486
Last Changed Date: 2020-06-09 00:49:49 -0400 (Tue, 09 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: primirTSS
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:primirTSS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings primirTSS_1.6.1.tar.gz
StartedAt: 2020-10-17 07:03:08 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:11:47 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 519.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: primirTSS.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:primirTSS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings primirTSS_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/primirTSS.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.6.1'
* package encoding: UTF-8
* 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 '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 ... WARNING
'::' or ':::' import not declared from: 'magrittr'
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/primirTSS.Rcheck/00check.log'
for details.



Installation output

primirTSS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/primirTSS_1.6.1.tar.gz && rm -rf primirTSS.buildbin-libdir && mkdir primirTSS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=primirTSS.buildbin-libdir primirTSS_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL primirTSS_1.6.1.zip && rm primirTSS_1.6.1.tar.gz primirTSS_1.6.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3676k  100 3676k    0     0  31.9M      0 --:--:-- --:--:-- --:--:-- 33.8M

install for i386

* installing *source* package 'primirTSS' ...
** using staged installation
** 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 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 'primirTSS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'primirTSS' as primirTSS_1.6.1.zip
* DONE (primirTSS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'primirTSS' successfully unpacked and MD5 sums checked

Tests output


Example timings

primirTSS.Rcheck/examples_i386/primirTSS-Ex.timings

nameusersystemelapsed
find_tss0.080.000.07
peak_join0.710.090.81
peak_merge0.080.090.18
plot_primiRNA0.020.020.03
run_primirTSSapp000
trans_cor0.500.071.31

primirTSS.Rcheck/examples_x64/primirTSS-Ex.timings

nameusersystemelapsed
find_tss0.080.000.08
peak_join0.520.000.51
peak_merge0.070.000.06
plot_primiRNA0.010.000.02
run_primirTSSapp000
trans_cor0.220.020.23