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: 0.99.29
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 46.92 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: SurfR_20231021180623
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

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* 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
--2023-10-21 14:08:59--  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, 2607:f220:41f:250::229, ...
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%  296M=0s

2023-10-21 14:09:00 (296 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 2023-10-21 14:10:21.5845122 is 2.090794137 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 2023-10-21 14:10:21.5848725 is 2.06178056 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 2023-10-21 14:10:22.0914476 is 2.538821804 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 2023-10-21 14:10:22.5639124 is 2.982340597 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 2023-10-21 14:10:23.094141 is 3.483666987 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 2023-10-21 14:10:23.5357661 is 3.896176828 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 2023-10-21 14:10:24.0541518 is 4.385578907 s in the future
--2023-10-21 14:10:24--  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)... 130.14.250.13, 130.14.250.11, 2607:f220:41f:250::230, ...
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: 15160 (15K) [application/x-gzip]
Saving to: ‘GSE58135_series_matrix.txt.gz’

     0K .......... ....                                       100% 1.12M=0.01s

2023-10-21 14:10:24 (1.12 MB/s) - ‘GSE58135_series_matrix.txt.gz’ saved [15160/15160]


Quitting from lines 616-623 [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: 0.99.29
 
                					
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 7.41 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: SurfR_20231021180623
 
                					
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
--2023-10-21 14:08:21--  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)... 165.112.9.230, 130.14.250.10
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: 3326 (3.2K) [application/x-gzip]
Saving to: ‘GSE121810_series_matrix.txt.gz’

     0K ...                                                   100% 96.1M=0s

2023-10-21 14:08:27 (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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