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CHECK report for HumanTranscriptomeCompendium on tokay2

This page was generated on 2019-10-16 12:44:08 -0400 (Wed, 16 Oct 2019).

Package 775/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HumanTranscriptomeCompendium 1.0.1
VJ Carey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/HumanTranscriptomeCompendium
Branch: RELEASE_3_9
Last Commit: 54511b0
Last Changed Date: 2019-09-25 06:27:59 -0400 (Wed, 25 Sep 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HumanTranscriptomeCompendium
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HumanTranscriptomeCompendium.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HumanTranscriptomeCompendium_1.0.1.tar.gz
StartedAt: 2019-10-16 04:28:46 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:34:18 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 331.8 seconds
RetCode: 0
Status:  OK  
CheckDir: HumanTranscriptomeCompendium.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HumanTranscriptomeCompendium.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HumanTranscriptomeCompendium_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/HumanTranscriptomeCompendium.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 'HumanTranscriptomeCompendium/DESCRIPTION' ... OK
* this is package 'HumanTranscriptomeCompendium' version '1.0.1'
* 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 'HumanTranscriptomeCompendium' 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 ... OK
* 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
htx_query_by_study_accession 9.41   0.37   11.15
htx_query_by_text            8.50   0.14    8.88
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
htx_query_by_study_accession 10.76   0.13   10.97
htx_query_by_text             7.75   0.18    8.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: OK


Installation output

HumanTranscriptomeCompendium.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/HumanTranscriptomeCompendium_1.0.1.tar.gz && rm -rf HumanTranscriptomeCompendium.buildbin-libdir && mkdir HumanTranscriptomeCompendium.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HumanTranscriptomeCompendium.buildbin-libdir HumanTranscriptomeCompendium_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL HumanTranscriptomeCompendium_1.0.1.zip && rm HumanTranscriptomeCompendium_1.0.1.tar.gz HumanTranscriptomeCompendium_1.0.1.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 1282k  100 1282k    0     0  19.1M      0 --:--:-- --:--:-- --:--:-- 21.2M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'HumanTranscriptomeCompendium' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HumanTranscriptomeCompendium'
    finding HTML links ... done
    HumanTranscriptomeCompendium.colnames   html  
    addRD                                   html  
    get_ds4841                              html  
    htx_app                                 html  
    htx_load                                html  
    htx_query_by_study_accession            html  
    htx_query_by_text                       html  
    load_bigrnaFiles                        html  
    load_experTable                         html  
    load_studTable                          html  
    path_doc4842                            html  
    procExpToGene                           html  
    tx2gene_gencode27                       html  
    uniqueAcc_120518                        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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'HumanTranscriptomeCompendium' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HumanTranscriptomeCompendium' as HumanTranscriptomeCompendium_1.0.1.zip
* DONE (HumanTranscriptomeCompendium)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'HumanTranscriptomeCompendium' successfully unpacked and MD5 sums checked

Tests output

HumanTranscriptomeCompendium.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(HumanTranscriptomeCompendium)
> 
> test_check("HumanTranscriptomeCompendium")
== testthat results  ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  38.93    4.79   47.64 

HumanTranscriptomeCompendium.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(HumanTranscriptomeCompendium)
> 
> test_check("HumanTranscriptomeCompendium")
== testthat results  ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  35.51    1.07   36.67 

Example timings

HumanTranscriptomeCompendium.Rcheck/examples_i386/HumanTranscriptomeCompendium-Ex.timings

nameusersystemelapsed
HumanTranscriptomeCompendium.colnames0.080.020.10
addRD000
get_ds48413.040.494.99
htx_app000
htx_load000
htx_query_by_study_accession 9.41 0.3711.15
htx_query_by_text8.500.148.88
load_bigrnaFiles000
load_experTable000
load_studTable000
path_doc48420.310.040.34
procExpToGene000
tx2gene_gencode270.530.031.66
uniqueAcc_1205180.070.000.06

HumanTranscriptomeCompendium.Rcheck/examples_x64/HumanTranscriptomeCompendium-Ex.timings

nameusersystemelapsed
HumanTranscriptomeCompendium.colnames0.110.030.14
addRD000
get_ds48413.560.173.73
htx_app000
htx_load000
htx_query_by_study_accession10.76 0.1310.97
htx_query_by_text7.750.188.03
load_bigrnaFiles000
load_experTable000
load_studTable000
path_doc48420.290.000.28
procExpToGene000
tx2gene_gencode270.310.000.31
uniqueAcc_1205180.030.020.05