Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/ginmappeR
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 22.04.3 LTS)/x86_64   OK     OK     skipped     OK  
merida1 macOS 12.7.1 Monterey/x86_64   OK     WARNINGS     OK     OK  

nebbiolo1 Summary

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Package: ginmappeR
Version: 0.99.9
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ginmappeR
BuildTime: 1 minutes 11.40 seconds
CheckCommand: BiocCheckGitClone('ginmappeR') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3124/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR.install-out.txt ginmappeR_0.99.9.tar.gz && BiocCheck('ginmappeR_0.99.9.tar.gz', `new-package`=TRUE)
CheckTime: 8 minutes 54.89 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 669.37 KiB
BuildID:: ginmappeR_20240212173944
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ginmappeR. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* preparing ‘ginmappeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘ginmappeR_0.99.9.tar.gz’


nebbiolo1 CHECK output

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===============================

 BiocCheckGitClone('ginmappeR')

===============================

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: ginmappeR
─ PackageVersion: 0.99.9
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
    * NOTE: (Optional) CITATION file not found. Only include a CITATION
      file if there is a preprint or publication for this Bioconductor
      package. Note that Bioconductor packages are not required to have
      a CITATION file but it is useful both for users and for tracking
      Bioconductor project-wide metrics. When including a CITATION
      file, add the publication using the 'doi' argument of
      'bibentry()'.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘0.99.9’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘ginmappeR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking whether startup messages can be suppressed ... [4s/4s] OK
* checking use of S3 registration ... 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 ... [17s/17s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 files in ‘vignettes’ ... OK
* checking examples ... [21s/107s] OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getCARD2KEGG           1.675  0.177  13.300
getCARD2UniProt        0.727  0.050   7.875
getKEGG2NCBINucleotide 0.552  0.004   7.311
getNCBINucleotide2KEGG 0.535  0.012   7.636
getNCBIGene2KEGG       0.514  0.027   7.753
getNCBIProtein2KEGG    0.425  0.016  11.610
getNCBIProtein2UniProt 0.234  0.001   5.076
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [26s/323s]
 [27s/323s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE

Status: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR.Rcheck/00check.log’
for details.






===============================

 BiocCheck('ginmappeR_0.99.9.tar.gz')

===============================

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: ginmappeR
─ PackageVersion: 0.99.9
─ sourceDir: /tmp/Rtmp3K9EbN/file1b43204b16403/ginmappeR
─ installDir: /tmp/Rtmp3K9EbN/file1b43205b5f11c0
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide 'URL', 'BugReports', 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ginmappeR...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 31 times)
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 29
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 4 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 88% of man pages use at least one of these tags.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 391 lines (11%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 355 lines
      (10%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package is in the Support Site Watched Tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 15 NOTES

See the ginmappeR.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

nebbiolo1 BUILD BIN output

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merida1 Summary

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Package: ginmappeR
Version: 0.99.9
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ginmappeR
BuildTime: 1 minutes 40.65 seconds
CheckCommand: BiocCheckGitClone('ginmappeR') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3124/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR.install-out.txt ginmappeR_0.99.9.tar.gz && BiocCheck('ginmappeR_0.99.9.tar.gz', `new-package`=TRUE)
CheckTime: 12 minutes 26.31 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh ginmappeR_0.99.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 40.86 seconds
PackageFileSize: 669.37 KiB
BuildID:: ginmappeR_20240212173944
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ginmappeR. Starting Build package. Starting Check package. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.WARNING: check time exceeded 10 min. Build Package status: 0.

merida1 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* preparing ‘ginmappeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘ginmappeR_0.99.9.tar.gz’


merida1 CHECK output

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===============================

 BiocCheckGitClone('ginmappeR')

===============================

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: ginmappeR
─ PackageVersion: 0.99.9
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
    * NOTE: (Optional) CITATION file not found. Only include a CITATION
      file if there is a preprint or publication for this Bioconductor
      package. Note that Bioconductor packages are not required to have
      a CITATION file but it is useful both for users and for tracking
      Bioconductor project-wide metrics. When including a CITATION
      file, add the publication using the 'doi' argument of
      'bibentry()'.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘0.99.9’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘ginmappeR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [10s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/11s] OK
* checking whether the package can be unloaded cleanly ... [10s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/11s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking whether startup messages can be suppressed ... [6s/6s] OK
* checking use of S3 registration ... 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 ... [42s/46s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 files in ‘vignettes’ ... OK
* checking examples ... [33s/159s] OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
getCARD2KEGG             3.649  0.178  20.131
getCARD2UniProt          0.658  0.065  16.360
getNCBINucleotide2KEGG   0.366  0.016  17.595
getNCBIGene2KEGG         0.358  0.014  10.198
getKEGG2NCBINucleotide   0.354  0.011   6.618
getNCBIProtein2UniProt   0.305  0.011   8.037
getNCBIProtein2KEGG      0.233  0.012  11.565
getNCBIIdenticalProteins 0.035  0.003  11.576
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [32s/325s]
 [32s/326s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [13s/15s] OK
* DONE

Status: 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR.Rcheck/00check.log’
for details.


 WARNING: R CMD check exceeded 10 min requirement






===============================

 BiocCheck('ginmappeR_0.99.9.tar.gz')

===============================

─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: ginmappeR
─ PackageVersion: 0.99.9
─ sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpsSl2pk/file775f1b6e899d/ginmappeR
─ installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpsSl2pk/file775f3b16d970
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3124/795321d2a95900f5bfbf349c9bbf197114e45394/ginmappeR.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide 'URL', 'BugReports', 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ginmappeR...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 31 times)
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 29
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 4 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 88% of man pages use at least one of these tags.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 391 lines (11%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 355 lines
      (10%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package is in the Support Site Watched Tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 15 NOTES

See the ginmappeR.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

merida1 BUILD BIN output

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===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir ginmappeR_0.99.9.tar.gz'
>>>>>>> 

* installing *source* package ‘ginmappeR’ ...
** using staged installation
** R
** 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 (ginmappeR)