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: 0.99.24

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: 4 minutes 54.67 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: SurfR_20231020181249

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 14:15:20--  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, 165.112.9.230, 2607:f220:41e:250::12, ...
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%  402M=0s

2023-10-20 14:15:20 (402 MB/s) - ‘GSE121810_series_matrix.txt.gz’ saved [3326/3326]

trying URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
/usr/bin/tar: MANIFEST.txt: time stamp 2023-10-20 14:16:22.8832946 is 5.85024679 s in the future
/usr/bin/tar: 9802559f-436d-4a6f-a98c-4652475bc5d4/323f4d00-a374-4398-aa8f-137de14ae7b5.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 14:16:22.8837585 is 5.820826009 s in the future
/usr/bin/tar: a38d8021-9400-4972-a996-740fa66d715f/56409e6d-e9d6-4ef6-b6a5-33642a84ef6c.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 14:16:23.5177324 is 6.425724968 s in the future
/usr/bin/tar: aa312284-657d-4a55-a7d9-a05d08faab2a/4202e326-1d5d-4a48-bac1-cf1fd4924515.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 14:16:24.041254 is 6.919468547 s in the future
/usr/bin/tar: defb5e95-edfb-4aa9-ba6f-6cd06fe91993/f648abc5-cf97-49f3-9197-3976ea7d37cf.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 14:16:24.5591044 is 7.407803882 s in the future
trying URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
--2023-10-20 14:17:18--  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)... 130.14.250.12, 130.14.250.13, 2607:f220:41f:250::228, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.12|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 15160 (15K) [application/x-gzip]
Saving to: ‘GSE58135_series_matrix.txt.gz’

     0K .......... ....                                       100% 1.11M=0.01s

2023-10-20 14:17:18 (1.11 MB/s) - ‘GSE58135_series_matrix.txt.gz’ saved [15160/15160]


Quitting from lines 536-550 [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: 0.99.24

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 7.29 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: SurfR_20231020181249

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 14:14:48--  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)... 130.14.250.13, 130.14.250.11
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.13|: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%  106M=0s

2023-10-20 14:14:55 (106 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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