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: 0.99.25

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 14.46 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: SurfR_20231020210910

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 17:12:27--  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)... 130.14.250.12, 165.112.9.228, 2607:f220:41e:250::7, ...
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: 3326 (3.2K) [application/x-gzip]
Saving to: ‘GSE121810_series_matrix.txt.gz’

     0K ...                                                   100%  357M=0s

2023-10-20 17:12:27 (357 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'
/usr/bin/tar: MANIFEST.txt: time stamp 2023-10-20 17:14:37.3491185 is 2.02720817 s in the future
/usr/bin/tar: 248ac510-a5af-4608-9cdc-5c8673633b82/d23ff3bc-5524-4dca-b0f4-a1561a30566c.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 17:14:37.3495471 is 1.998366368 s in the future
/usr/bin/tar: 4df2233b-3bbc-4d20-9abc-2a09b3f37383/eb0f8bc7-5f47-4174-8e85-678bd011bc3c.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 17:14:37.8468497 is 2.465550837 s in the future
/usr/bin/tar: 6b62d6dd-bb6f-4f39-9041-992c47b875f3/d1f7678a-8106-46c9-95b7-5ec5d940f08c.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 17:14:38.2969787 is 2.886209135 s in the future
/usr/bin/tar: 90eefb33-6808-45c3-9ab1-6eca0decdc9d/71c9a6fc-0538-4533-af51-f7c9defe7770.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 17:14:38.767951 is 3.327903092 s in the future
/usr/bin/tar: eddb2dc6-2b72-43a8-a7fc-3dd09dde68af/316d8a79-9084-4355-9de7-e29503bf0864.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 17:14:39.2611058 is 3.791486293 s in the future
/usr/bin/tar: f66aace4-01a4-4def-8e71-26d9aaf13d49/9db2f825-0d02-4437-9107-a6b92ef4e2cc.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-20 17:14:39.7265294 is 4.227504527 s in the future
--2023-10-20 17:14:39--  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, 130.14.250.7, 2607:f220:41f:250::229, ...
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

2023-10-20 17:14:39 (1.22 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: 0.99.25

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 37.48 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: SurfR_20231020210910

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 17:12:12--  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% 96.1M=0s

2023-10-20 17:12:12 (96.1 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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