Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/DESpace

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
merida1	macOS 10.14.6 Mojave/x86_64	OK	ERROR	ERROR	OK
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)/x86_64	ERROR	skipped	skipped	skipped

merida1 Summary

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Package: DESpace

Version: 0.99.1

RVersion: 4.3

BiocVersion: 3.17

BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DESpace

BuildTime: 9 minutes 15.35 seconds

CheckCommand: BiocCheckGitClone('DESpace') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2946/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2946/fe29b12a206e83d5a34a6402f77f0c36b904f05d/DESpace.install-out.txt DESpace_0.99.1.tar.gz && BiocCheck('DESpace_0.99.1.tar.gz', `new-package`=TRUE)

CheckTime: 8 minutes 37.18 seconds

BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh DESpace_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir

BuildBinTime: 0 minutes 43.61 seconds

PackageFileSize: 463472.20 KiB

BuildID:: DESpace_20230303194756

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DESpace. 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. Checking Package status: 1. Build Package status: 1.

merida1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘DESpace/DESCRIPTION’ ... OK
* preparing ‘DESpace’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘DESpace_0.99.1.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/expression plots all cluster_6c7340b1589ea1e0d7419cfaa21f080f.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/expression plots all cluster_6c7340b1589ea1e0d7419cfaa21f080f.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/expression plots all cluster_6c7340b1589ea1e0d7419cfaa21f080f.rdx’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/expression plots high_low_0dc11ca19dfa1f1775fb94e7b27f69af.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_0c3dac2f84f07b57f211211646ddef1d.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_0c3dac2f84f07b57f211211646ddef1d.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_0c3dac2f84f07b57f211211646ddef1d.rdx’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_0f43e5a9c96822dc4c37d9f7e9863fcb.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_0f43e5a9c96822dc4c37d9f7e9863fcb.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_0f43e5a9c96822dc4c37d9f7e9863fcb.rdx’

merida1 CHECK output

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

 BiocCheckGitClone('DESpace')

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

─ BiocCheckVersion: 1.35.12
─ BiocVersion: 3.17
─ Package: DESpace
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2946/fe29b12a206e83d5a34a6402f77f0c36b904f05d/DESpace
─ 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/2946/fe29b12a206e83d5a34a6402f77f0c36b904f05d/DESpace.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESpace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESpace’ version ‘0.99.1’
* 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 ... WARNING
Found the following files with non-portable file names:
  vignettes/DESpace_cache/html/DESpace [multi]_b311451acc07348367c84f6777caaf4d.RData
  vignettes/DESpace_cache/html/DESpace [multi]_b311451acc07348367c84f6777caaf4d.rdb
  vignettes/DESpace_cache/html/DESpace [multi]_b311451acc07348367c84f6777caaf4d.rdx
  vignettes/DESpace_cache/html/QC genes_19078e38e1ba27175d04eb7b71cb3ea3.RData
  vignettes/DESpace_cache/html/QC genes_19078e38e1ba27175d04eb7b71cb3ea3.rdb
  vignettes/DESpace_cache/html/QC genes_19078e38e1ba27175d04eb7b71cb3ea3.rdx
  vignettes/DESpace_cache/html/QC spots_425f5238613d1be8d25e02be8ba3e8d4.RData
  vignettes/DESpace_cache/html/QC spots_425f5238613d1be8d25e02be8ba3e8d4.rdb
  vignettes/DESpace_cache/html/QC spots_425f5238613d1be8d25e02be8ba3e8d4.rdx
  vignettes/DESpace_cache/html/expression plots all cluster_6c7340b1589ea1e0d7419cfaa21f080f.RData
  vignettes/DESpace_cache/html/expression plots all cluster_6c7340b1589ea1e0d7419cfaa21f080f.rdb
  vignettes/DESpace_cache/html/expression plots all cluster_6c7340b1589ea1e0d7419cfaa21f080f.rdx
  vignettes/DESpace_cache/html/expression plots high_low_0dc11ca19dfa1f1775fb94e7b27f69af.RData
  vignettes/DESpace_cache/html/expression plots high_low_0dc11ca19dfa1f1775fb94e7b27f69af.rdb
  vignettes/DESpace_cache/html/expression plots high_low_0dc11ca19dfa1f1775fb94e7b27f69af.rdx
  vignettes/DESpace_cache/html/free memory_53135e4e49a8a7dd69ff732bbdf6de0d.RData
  vignettes/DESpace_cache/html/free memory_53135e4e49a8a7dd69ff732bbdf6de0d.rdb
  vignettes/DESpace_cache/html/free memory_53135e4e49a8a7dd69ff732bbdf6de0d.rdx
  vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_0c3dac2f84f07b57f211211646ddef1d.RData
  vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_0c3dac2f84f07b57f211211646ddef1d.rdb
  vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_0c3dac2f84f07b57f211211646ddef1d.rdx
  vignettes/DESpace_cache/html/individual cluster test_b001cc0698e7d08e71e5dff635d33355.RData
  vignettes/DESpace_cache/html/individual cluster test_b001cc0698e7d08e71e5dff635d33355.rdb
  vignettes/DESpace_cache/html/individual cluster test_b001cc0698e7d08e71e5dff635d33355.rdx
  vignettes/DESpace_cache/html/show top results high_d7da1de50eb28badb6ef7054b06d9593.RData
  vignettes/DESpace_cache/html/show top results high_d7da1de50eb28badb6ef7054b06d9593.rdb
  vignettes/DESpace_cache/html/show top results high_d7da1de50eb28badb6ef7054b06d9593.rdx
  vignettes/DESpace_cache/html/show top results low_97da5aa11e87f8e001f44e9c19a60851.RData
  vignettes/DESpace_cache/html/show top results low_97da5aa11e87f8e001f44e9c19a60851.rdb
  vignettes/DESpace_cache/html/show top results low_97da5aa11e87f8e001f44e9c19a60851.rdx
  vignettes/DESpace_cache/html/stLearn[py multi-sample]_6a19de47dd9165ed29791ce9d75cb98e.RData
  vignettes/DESpace_cache/html/stLearn[py multi-sample]_6a19de47dd9165ed29791ce9d75cb98e.rdb
  vignettes/DESpace_cache/html/stLearn[py multi-sample]_6a19de47dd9165ed29791ce9d75cb98e.rdx
  vignettes/DESpace_cache/html/stLearn[r multi-sample]_093cdf313da47442a8c983a7659de2e3.RData
  vignettes/DESpace_cache/html/stLearn[r multi-sample]_093cdf313da47442a8c983a7659de2e3.rdb
  vignettes/DESpace_cache/html/stLearn[r multi-sample]_093cdf313da47442a8c983a7659de2e3.rdx
  vignettes/DESpace_cache/html/top SVGs expression plot [multi]_0f43e5a9c96822dc4c37d9f7e9863fcb.RData
  vignettes/DESpace_cache/html/top SVGs expression plot [multi]_0f43e5a9c96822dc4c37d9f7e9863fcb.rdb
  vignettes/DESpace_cache/html/top SVGs expression plot [multi]_0f43e5a9c96822dc4c37d9f7e9863fcb.rdx
  vignettes/DESpace_cache/html/top SVGs expression plot_3eab973e549ebeb39adf9f05d3e38887.RData
  vignettes/DESpace_cache/html/top SVGs expression plot_3eab973e549ebeb39adf9f05d3e38887.rdb
  vignettes/DESpace_cache/html/top SVGs expression plot_3eab973e549ebeb39adf9f05d3e38887.rdx
  vignettes/DESpace_cache/html/top results WM_6e6327aeab96726a0455f7fab1d0b773.RData
  vignettes/DESpace_cache/html/top results WM_6e6327aeab96726a0455f7fab1d0b773.rdb
  vignettes/DESpace_cache/html/top results WM_6e6327aeab96726a0455f7fab1d0b773.rdx
  vignettes/DESpace_cache/html/top results all_2329c2ff4d9a5ac7b805f0b4816a20cf.RData
  vignettes/DESpace_cache/html/top results all_2329c2ff4d9a5ac7b805f0b4816a20cf.rdb
  vignettes/DESpace_cache/html/top results all_2329c2ff4d9a5ac7b805f0b4816a20cf.rdx
  vignettes/DESpace_cache/html/top results high_low_10f8acd1fd7ca470b9026a91448ded1e.RData
  vignettes/DESpace_cache/html/top results high_low_10f8acd1fd7ca470b9026a91448ded1e.rdb
  vignettes/DESpace_cache/html/top results high_low_10f8acd1fd7ca470b9026a91448ded1e.rdx
  vignettes/DESpace_cache/html/view LIBD layers [multi]_90ca02cbcc16dfe3b6b5c8cbb013dc04.RData
  vignettes/DESpace_cache/html/view LIBD layers [multi]_90ca02cbcc16dfe3b6b5c8cbb013dc04.rdb
  vignettes/DESpace_cache/html/view LIBD layers [multi]_90ca02cbcc16dfe3b6b5c8cbb013dc04.rdx
  vignettes/DESpace_cache/html/view LIBD layers_bb53e73c98ee68ab5c18f9da13be37ff.RData
  vignettes/DESpace_cache/html/view LIBD layers_bb53e73c98ee68ab5c18f9da13be37ff.rdb
  vignettes/DESpace_cache/html/view LIBD layers_bb53e73c98ee68ab5c18f9da13be37ff.rdx
  vignettes/DESpace_cache/html/visualize colData_f1d2ec2808be88c042cbd9da6c6f5558.RData
  vignettes/DESpace_cache/html/visualize colData_f1d2ec2808be88c042cbd9da6c6f5558.rdb
  vignettes/DESpace_cache/html/visualize colData_f1d2ec2808be88c042cbd9da6c6f5558.rdx
  vignettes/DESpace_cache/html/visualize results WM_a3f1054b86be6c9cd031ebc2805f9ebf.RData
  vignettes/DESpace_cache/html/visualize results WM_a3f1054b86be6c9cd031ebc2805f9ebf.rdb
  vignettes/DESpace_cache/html/visualize results WM_a3f1054b86be6c9cd031ebc2805f9ebf.rdx
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Found the following non-portable file paths:
  DESpace/vignettes/DESpace_cache/html/expression plots all cluster_6c7340b1589ea1e0d7419cfaa21f080f.RData
  DESpace/vignettes/DESpace_cache/html/expression plots all cluster_6c7340b1589ea1e0d7419cfaa21f080f.rdb
  DESpace/vignettes/DESpace_cache/html/expression plots all cluster_6c7340b1589ea1e0d7419cfaa21f080f.rdx
  DESpace/vignettes/DESpace_cache/html/expression plots high_low_0dc11ca19dfa1f1775fb94e7b27f69af.RData
  DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_0c3dac2f84f07b57f211211646ddef1d.RData
  DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_0c3dac2f84f07b57f211211646ddef1d.rdb
  DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_0c3dac2f84f07b57f211211646ddef1d.rdx
  DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_0f43e5a9c96822dc4c37d9f7e9863fcb.RData
  DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_0f43e5a9c96822dc4c37d9f7e9863fcb.rdb
  DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_0f43e5a9c96822dc4c37d9f7e9863fcb.rdx

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DESpace’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [31s/31s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [111s/156s] OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
DESpace_test    44.293  1.878  55.870
individual_test 25.434  0.651  58.951
FeaturePlot     23.200  0.518  25.729
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testhat.R’ [139s/145s]
 [139s/145s] 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 ... [6s/6s] OK
* DONE

Status: 1 WARNING
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2946/fe29b12a206e83d5a34a6402f77f0c36b904f05d/DESpace.Rcheck/00check.log’
for details.






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

 BiocCheck('DESpace_0.99.1.tar.gz')

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

Error: package or namespace load failed for ‘BiocCheck’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘graph’
Execution halted

merida1 BUILD BIN output

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DESpace_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘DESpace’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘sparseMatrixStats’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘DESpace’
* removing ‘/Users/pkgbuild/packagebuilder/workers/jobs/2946/fe29b12a206e83d5a34a6402f77f0c36b904f05d/libdir/DESpace’

nebbiolo1 Summary

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Package: DESpace

Version: 0.99.1

RVersion: 4.3

BiocVersion: 3.17

BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DESpace

BuildTime: 8 minutes 9.90 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: DESpace_20230303194756

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DESpace. 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: 1.

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘DESpace/DESCRIPTION’ ... OK
* preparing ‘DESpace’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DESpace.Rmd’ using rmarkdown
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: processing vignette 'DESpace.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘DESpace.Rmd’

SUMMARY: processing the following file failed:
  ‘DESpace.Rmd’

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output

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