Bioconductor Single Package Builder - Build History

Snapshot Date:

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

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 20.04.4 LTS)/x86_64	ERROR	skipped	skipped	skipped
merida1	/	ERROR	skipped	skipped	skipped

nebbiolo1 Summary

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Package: stJoincount

Version: 0.99.0

RVersion: 4.2

BiocVersion: 3.15

BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data stJoincount

BuildTime: 0 minutes 33.06 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: stJoincount_20220418145602

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: stJoincount. 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 ‘stJoincount/DESCRIPTION’ ... OK
* preparing ‘stJoincount’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stJoincount-vignette.Rmd’ using rmarkdown
Loading required package: dbplyr
Loading required package: sp
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1; sf_use_s2() is TRUE
Attaching SeuratObject
adding rname 'https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Breast_Cancer_Block_A_Section_1/V1_Breast_Cancer_Block_A_Section_1_filtered_feature_bc_matrix.tar.gz'
adding rname 'https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Breast_Cancer_Block_A_Section_1/V1_Breast_Cancer_Block_A_Section_1_spatial.tar.gz'
adding rname 'https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Breast_Cancer_Block_A_Section_1/V1_Breast_Cancer_Block_A_Section_1_analysis.tar.gz'
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 26.8M    0  9132    0     0  83018      0  0:05:39 --:--:--  0:05:39 82270
100 26.8M  100 26.8M    0     0  32.4M      0 --:--:-- --:--:-- --:--:-- 32.4M
Quitting from lines 66-68 (stJoincount-vignette.Rmd) 
Error: processing vignette 'stJoincount-vignette.Rmd' failed with diagnostics:
Please install hdf5r to read HDF5 files
--- failed re-building ‘stJoincount-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘stJoincount-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output

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merida1 Summary

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Package: stJoincount

Version: 0.99.0

RVersion:

BiocVersion: 3.15

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

BuildTime: 0 minutes 57.49 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: stJoincount_20220418145602

PreProcessing: Installing dependencies. Checking Git Clone. Installing package: stJoincount. 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.

merida1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘stJoincount/DESCRIPTION’ ... OK
* preparing ‘stJoincount’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stJoincount-vignette.Rmd’ using rmarkdown
Loading required package: dbplyr
Loading required package: sp
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 8.2.1; sf_use_s2() is TRUE
Attaching SeuratObject
adding rname 'https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Breast_Cancer_Block_A_Section_1/V1_Breast_Cancer_Block_A_Section_1_filtered_feature_bc_matrix.tar.gz'
adding rname 'https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Breast_Cancer_Block_A_Section_1/V1_Breast_Cancer_Block_A_Section_1_spatial.tar.gz'
adding rname 'https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Breast_Cancer_Block_A_Section_1/V1_Breast_Cancer_Block_A_Section_1_analysis.tar.gz'
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 15 26.8M   15 4396k    0     0  3779k      0  0:00:07  0:00:01  0:00:06 3777k
100 26.8M  100 26.8M    0     0  15.1M      0  0:00:01  0:00:01 --:--:-- 15.1M
Quitting from lines 66-68 (stJoincount-vignette.Rmd) 
Error: processing vignette 'stJoincount-vignette.Rmd' failed with diagnostics:
Please install hdf5r to read HDF5 files
--- failed re-building ‘stJoincount-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘stJoincount-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

merida1 CHECK output

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merida1 BUILD BIN output

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