Bioconductor Single Package Builder - Build History

Snapshot Date:

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

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo2	Linux (Ubuntu 22.04.2 LTS)/x86_64	ERROR	skipped	skipped	skipped
lconway	macOS 12.6.5 Monterey/x86_64	ERROR	skipped	skipped	skipped

nebbiolo2 Summary

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Package: SurfR

Version: 0.99.26

RVersion: 4.3

BiocVersion: 3.18

BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SurfR

BuildTime: 5 minutes 41.87 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: SurfR_20231020211132

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SurfR. 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.

nebbiolo2 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘SurfR/DESCRIPTION’ ... OK
* preparing ‘SurfR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Intro_to_SurfR.Rmd’ using rmarkdown
--2023-10-20 17:14:26--  https://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121810/matrix/GSE121810_series_matrix.txt.gz
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.7, 165.112.9.230, 2607:f220:41f:250::228, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.7|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3326 (3.2K) [application/x-gzip]
Saving to: ‘GSE121810_series_matrix.txt.gz’

     0K ...                                                   100%  371M=0s

2023-10-20 17:14:26 (371 MB/s) - ‘GSE121810_series_matrix.txt.gz’ saved [3326/3326]

trying URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
trying URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
--2023-10-20 17:16:30--  https://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58135/matrix/GSE58135_series_matrix.txt.gz
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.7, 130.14.250.11, 2607:f220:41e:250::10, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.7|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 15160 (15K) [application/x-gzip]
Saving to: ‘GSE58135_series_matrix.txt.gz’

     0K .......... ....                                       100% 1.07M=0.01s

2023-10-20 17:16:30 (1.07 MB/s) - ‘GSE58135_series_matrix.txt.gz’ saved [15160/15160]


Quitting from lines 639-646 [unnamed-chunk-11] (Intro_to_SurfR.Rmd)
Error: processing vignette 'Intro_to_SurfR.Rmd' failed with diagnostics:
unable to find an inherited method for function 'plotPCA' for signature '"missing"'
--- failed re-building ‘Intro_to_SurfR.Rmd’

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

Error: Vignette re-building failed.
Execution halted

nebbiolo2 CHECK output

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nebbiolo2 BUILD BIN output

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lconway Summary

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Package: SurfR

Version: 0.99.26

RVersion: 4.3

BiocVersion: 3.18

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

BuildTime: 1 minutes 45.08 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: SurfR_20231020211132

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SurfR. 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.

lconway BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘SurfR/DESCRIPTION’ ... OK
* preparing ‘SurfR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Intro_to_SurfR.Rmd’ using rmarkdown
--2023-10-20 17:14:54--  https://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121810/matrix/GSE121810_series_matrix.txt.gz
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 165.112.9.228, 130.14.250.12
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|165.112.9.228|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3326 (3.2K) [application/x-gzip]
Saving to: ‘GSE121810_series_matrix.txt.gz’

     0K ...                                                   100% 99.1M=0s

2023-10-20 17:14:54 (99.1 MB/s) - ‘GSE121810_series_matrix.txt.gz’ saved [3326/3326]


Quitting from lines 183-211 [GEO input] (Intro_to_SurfR.Rmd)
Error: processing vignette 'Intro_to_SurfR.Rmd' failed with diagnostics:
Rhdf5lib was not compiled with support for the S3 VFD

--- failed re-building ‘Intro_to_SurfR.Rmd’

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

Error: Vignette re-building failed.
Execution halted

lconway CHECK output

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lconway BUILD BIN output

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