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: 0.99.16

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: 6 minutes 34.56 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: SurfR_20231009212926

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
--2023-10-09 17:32:29--  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, 165.112.9.230, 2607:f220:41e:250::7, ...
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%  336M=0s

2023-10-09 17:32:29 (336 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'
--2023-10-09 17:35:10--  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)... 165.112.9.230, 165.112.9.229, 2607:f220:41e:250::13, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|165.112.9.230|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 15160 (15K) [application/x-gzip]
Saving to: ‘GSE58135_series_matrix.txt.gz’

     0K .......... ....                                       100% 1.22M=0.01s

2023-10-09 17:35:10 (1.22 MB/s) - ‘GSE58135_series_matrix.txt.gz’ saved [15160/15160]


Quitting from lines 507-522 [unnamed-chunk-6] (Intro_to_SurfR.Rmd)
Error: processing vignette 'Intro_to_SurfR.Rmd' failed with diagnostics:
OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
--- 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: 0.99.16

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: 2 minutes 4.99 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: SurfR_20231009212926

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
--2023-10-09 17:32:54--  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)... 165.112.9.229, 130.14.250.13
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|165.112.9.229|: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% 85.7M=0s

2023-10-09 17:32:54 (85.7 MB/s) - ‘GSE121810_series_matrix.txt.gz’ saved [3326/3326]


Quitting from lines 169-192 [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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