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This page was generated on 2023-01-02 09:00:19 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for BaseSpaceR on palomino5


To the developers/maintainers of the BaseSpaceR package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 114/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BaseSpaceR 1.43.0  (landing page)
Jared O'Connell
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/BaseSpaceR
git_branch: master
git_last_commit: 56a2e06
git_last_commit_date: 2022-11-01 11:08:02 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: BaseSpaceR
Version: 1.43.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BaseSpaceR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BaseSpaceR_1.43.0.tar.gz
StartedAt: 2022-12-28 21:44:35 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 21:45:30 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 55.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BaseSpaceR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BaseSpaceR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BaseSpaceR_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BaseSpaceR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BaseSpaceR/DESCRIPTION' ... OK
* this is package 'BaseSpaceR' version '1.43.0'
* 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 ... OK
* 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
* 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 ... WARNING
checkRd: (5) Genomes-class.Rd:49-52: \item in \describe must have non-empty label
checkRd: (5) Genomes-class.Rd:53-58: \item in \describe must have non-empty label
checkRd: (5) Genomes-class.Rd:59-62: \item in \describe must have non-empty label
checkRd: (5) Projects-class.Rd:55-58: \item in \describe must have non-empty label
checkRd: (5) Projects-class.Rd:59-64: \item in \describe must have non-empty label
checkRd: (5) Projects-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) Runs-class.Rd:55-58: \item in \describe must have non-empty label
checkRd: (5) Runs-class.Rd:59-64: \item in \describe must have non-empty label
checkRd: (5) Runs-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) Samples-class.Rd:63-66: \item in \describe must have non-empty label
checkRd: (5) Samples-class.Rd:67-72: \item in \describe must have non-empty label
checkRd: (5) Samples-class.Rd:73-76: \item in \describe must have non-empty label
checkRd: (5) Users-class.Rd:33-36: \item in \describe must have non-empty label
checkRd: (5) Users-class.Rd:37-41: \item in \describe must have non-empty label
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Runs-class 0.11   0.02    6.32
* 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, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BaseSpaceR.Rcheck/00check.log'
for details.



Installation output

BaseSpaceR.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL BaseSpaceR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'BaseSpaceR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (BaseSpaceR)

Tests output


Example timings

BaseSpaceR.Rcheck/BaseSpaceR-Ex.timings

nameusersystemelapsed
AppAuth-class0.100.051.18
AppResults-class000
AppSessionAuth000
AppSessions-class000
Coverage000
Error000
Files-class0.050.001.42
FilesExtra0.060.000.80
Genomes-class0.130.000.99
Projects-class0.090.001.78
Response-class000
Runs-class0.110.026.32
Samples-class0.060.012.61
ServiceURI-class000
Users-class0.070.000.41
Variants0.040.001.88
data-aAuth0.020.030.14