lconway Summary
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| Package: MGnifyR |
| Version: 0.99.2 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MGnifyR |
| BuildTime: 52 minutes 37.07 seconds |
| CheckCommand: BiocCheckGitClone('MGnifyR') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3191/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR.install-out.txt MGnifyR_0.99.2.tar.gz && BiocCheck('MGnifyR_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 2.47 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh MGnifyR_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 3.48 seconds |
| PackageFileSize: 58978.35 KiB |
| BuildID:: MGnifyR_20231115124251 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MGnifyR. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. 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: 1. Build Package status: 1. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘MGnifyR/DESCRIPTION’ ... OK
* preparing ‘MGnifyR’:
* 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 ‘MGnifyR_0.99.2.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/analyses/MGYA00096989/file/ERR1809133_MERGED_FASTQ_CDS_annotated.faa.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/analyses/MGYA00144458/file/ERR2270676_MERGED_FASTQ_CDS_annotated.faa.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/samples_format_biome_name_json_root:Environmental:Aquatic:Freshwater:Drinking water/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/samples_format_biome_name_json_root:Environmental:Aquatic:Freshwater:Drinking water/.RDS’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/samples_format_latitude_gte_experiment_type_biome_name_instrument_platform_json_60_amplicon_Soil_Illumina/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/samples_format_latitude_gte_experiment_type_biome_name_instrument_platform_json_60_amplicon_Soil_Illumina/.RDS’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
using GNU extension for long pathname
lconway CHECK output
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===============================
BiocCheckGitClone('MGnifyR')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: MGnifyR
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR
─ 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...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
Warning in file(name, "wb") :
cannot open file 'MGnifyR/inst/extdata/mgnify_cache/samples_format_latitude_gte_experiment_type_biome_name_instrument_platform_json_60_amplicon_Soil_Illumina/': No such file or directory
Error in file(name, "wb") : cannot open the connection
Execution halted
===============================
BiocCheck('MGnifyR_0.99.2.tar.gz')
===============================
* ERROR:
/Users/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR_0.99.2.tar.gz
must be installable.
* ERROR:
/Users/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR_0.99.2.tar.gz
must be loadable.
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: MGnifyR
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpABFvRi/file3d9c6f3422fd/MGnifyR
─ installDir: /tmp/RtmpABFvRi/file3d9c1e20e4ec
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR.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...
* WARNING: Package files exceed the 5MB size limit.
* WARNING: Data files exceed the 5MB size limit.
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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...
* 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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
no package 'MGnifyR' was found
Error in pkg_desc$Imports : $ operator is invalid for atomic vectors
Calls: BiocCheck ... checkDescriptionNamespaceConsistency -> cleanupDependency
Execution halted
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir MGnifyR_0.99.2.tar.gz'
>>>>>>>
Warning in file(name, "wb") :
cannot open file 'MGnifyR/inst/extdata/mgnify_cache/samples_format_latitude_gte_experiment_type_biome_name_instrument_platform_json_60_amplicon_Soil_Illumina/': No such file or directory
Error in file(name, "wb") : cannot open the connection
nebbiolo2 Summary
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| Package: MGnifyR |
| Version: 0.99.2 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MGnifyR |
| BuildTime: 52 minutes 50.66 seconds |
| CheckCommand: BiocCheckGitClone('MGnifyR') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3191/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR.install-out.txt MGnifyR_0.99.2.tar.gz && BiocCheck('MGnifyR_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 2.79 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 58966.33 KiB |
| BuildID:: MGnifyR_20231115124251 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MGnifyR. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. 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: 1. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘MGnifyR/DESCRIPTION’ ... OK
* preparing ‘MGnifyR’:
* 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 ‘MGnifyR_0.99.2.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/analyses/MGYA00096989/file/ERR1809133_MERGED_FASTQ_CDS_annotated.faa.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/analyses/MGYA00144458/file/ERR2270676_MERGED_FASTQ_CDS_annotated.faa.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/samples_format_biome_name_json_root:Environmental:Aquatic:Freshwater:Drinking water/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/samples_format_biome_name_json_root:Environmental:Aquatic:Freshwater:Drinking water/.RDS’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/samples_format_latitude_gte_experiment_type_biome_name_instrument_platform_json_60_amplicon_Soil_Illumina/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘MGnifyR/inst/extdata/mgnify_cache/samples_format_latitude_gte_experiment_type_biome_name_instrument_platform_json_60_amplicon_Soil_Illumina/.RDS’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
using GNU extension for long pathname
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('MGnifyR')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: MGnifyR
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR
─ 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...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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
Warning in file(name, "wb") :
cannot open file 'MGnifyR/inst/extdata/mgnify_cache/samples_format_latitude_gte_experiment_type_biome_name_instrument_platform_json_60_amplicon_Soil_Illumina/': Is a directory
Error in file(name, "wb") : cannot open the connection
Execution halted
===============================
BiocCheck('MGnifyR_0.99.2.tar.gz')
===============================
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR_0.99.2.tar.gz
must be installable.
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR_0.99.2.tar.gz
must be loadable.
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: MGnifyR
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpS9Zho7/file944b36dc3158c/MGnifyR
─ installDir: /tmp/RtmpS9Zho7/file944b325cff9ce
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3191/f1a23cbc13ec8eede7068eda56e76d3e1012912c/MGnifyR.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...
* WARNING: Package files exceed the 5MB size limit.
* WARNING: Data files exceed the 5MB size limit.
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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...
* 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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
no package 'MGnifyR' was found
Error in pkg_desc$Imports : $ operator is invalid for atomic vectors
Calls: BiocCheck ... checkDescriptionNamespaceConsistency -> cleanupDependency
Execution halted
nebbiolo2 BUILD BIN output
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