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CHECK report for BaseSpaceR on riesling1

This page was generated on 2020-10-28 13:27:52 -0400 (Wed, 28 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BaseSpaceR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 117/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BaseSpaceR 1.34.0
Jared O'Connell
Snapshot Date: 2020-10-27 13:12:07 -0400 (Tue, 27 Oct 2020)
URL: https://git.bioconductor.org/packages/BaseSpaceR
Branch: RELEASE_3_12
Last Commit: 40c323f
Last Changed Date: 2020-10-27 10:49:55 -0400 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: BaseSpaceR
Version: 1.34.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaseSpaceR.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BaseSpaceR_1.34.0.tar.gz
StartedAt: 2020-10-27 20:06:28 -0400 (Tue, 27 Oct 2020)
EndedAt: 2020-10-27 20:07:26 -0400 (Tue, 27 Oct 2020)
EllapsedTime: 57.4 seconds
RetCode: 0
Status:  OK  
CheckDir: BaseSpaceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaseSpaceR.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BaseSpaceR_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/BaseSpaceR.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 'BaseSpaceR/DESCRIPTION' ... OK
* this is package 'BaseSpaceR' version '1.34.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'BaseSpaceR' 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 ... NOTE
'library' or 'require' call to 'Rsamtools' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
asBamFile: no visible global function definition for 'BamFile'
GET,ServiceURI: no visible global function definition for
  'basicHeaderGatherer'
GET,ServiceURI: no visible global function definition for
  'basicTextGatherer'
GET,ServiceURI: no visible global function definition for 'getForm'
GET,ServiceURI: no visible global function definition for 'curlOptions'
POST,ServiceURI: no visible global function definition for
  'basicHeaderGatherer'
POST,ServiceURI: no visible global function definition for
  'basicTextGatherer'
POST,ServiceURI: no visible global function definition for
  'curlPerform'
POSTForm,ServiceURI: no visible global function definition for
  'basicHeaderGatherer'
POSTForm,ServiceURI: no visible global function definition for
  'basicTextGatherer'
POSTForm,ServiceURI: no visible global function definition for
  'postForm'
POSTForm,ServiceURI: no visible global function definition for
  'curlOptions'
getBAMs,AppResults: no visible binding for global variable
  'BamFileList'
getFiles,AppAuth : .toDisk: no visible global function definition for
  'CFILE'
getFiles,AppAuth : .toDisk: no visible global function definition for
  'curlPerform'
getFiles,AppAuth : .toMem: no visible global function definition for
  'getURLContent'
getFiles,AppAuth : .toMem: no visible binding for global variable
  'dsize'
Undefined global functions or variables:
  BamFile BamFileList CFILE basicHeaderGatherer basicTextGatherer
  curlOptions curlPerform dsize getForm getURLContent postForm
* 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
** 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.12-bioc/meat/BaseSpaceR.Rcheck/00check.log'
for details.



Installation output

BaseSpaceR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/BaseSpaceR_1.34.0.tar.gz && rm -rf BaseSpaceR.buildbin-libdir && mkdir BaseSpaceR.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BaseSpaceR.buildbin-libdir BaseSpaceR_1.34.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BaseSpaceR_1.34.0.zip && rm BaseSpaceR_1.34.0.tar.gz BaseSpaceR_1.34.0.zip
###
##############################################################################
##############################################################################


  % 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  272k  100  272k    0     0  1059k      0 --:--:-- --:--:-- --:--:-- 1063k

install for i386

* installing *source* package 'BaseSpaceR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BaseSpaceR'
    finding HTML links ... done
    AppAuth-class                           html  
    AppResults-class                        html  
    AppSessionAuth                          html  
    AppSessions-class                       html  
    BaseSpaceR-package                      html  
    Coverage                                html  
    Error                                   html  
    Files-class                             html  
    FilesExtra                              html  
    Genomes-class                           html  
    Projects-class                          html  
    Response-class                          html  
    Runs-class                              html  
    Samples-class                           html  
    ServiceURI-class                        html  
    Users-class                             html  
    Variants                                html  
    data-aAuth                              html  
    private_methods                         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 'BaseSpaceR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BaseSpaceR' as BaseSpaceR_1.34.0.zip
* DONE (BaseSpaceR)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'BaseSpaceR' successfully unpacked and MD5 sums checked

Tests output


Example timings

BaseSpaceR.Rcheck/examples_i386/BaseSpaceR-Ex.timings

nameusersystemelapsed
AppAuth-class0.170.050.86
AppResults-class000
AppSessionAuth000
AppSessions-class000
Coverage000
Error000
Files-class0.040.000.68
FilesExtra0.030.000.59
Genomes-class0.100.000.81
Projects-class0.080.000.88
Response-class000
Runs-class0.070.002.00
Samples-class0.020.011.14
ServiceURI-class000
Users-class0.050.000.44
Variants0.030.000.66
data-aAuth0.030.000.30

BaseSpaceR.Rcheck/examples_x64/BaseSpaceR-Ex.timings

nameusersystemelapsed
AppAuth-class0.260.111.20
AppResults-class000
AppSessionAuth000
AppSessions-class000
Coverage000
Error000
Files-class0.050.000.70
FilesExtra0.050.021.05
Genomes-class0.060.001.01
Projects-class0.080.001.31
Response-class000
Runs-class0.150.002.23
Samples-class0.080.001.55
ServiceURI-class000
Users-class0.030.001.38
Variants0.030.001.35
data-aAuth0.030.011.01