lconway Summary
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| Package: SurfR |
| Version: 0.99.12 |
| 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 8.46 seconds |
| CheckCommand: |
| CheckTime: |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: -1.00 KiB |
| BuildID:: SurfR_20230928191933 |
| 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
--2023-09-28 15:23:26-- 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)... 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% 70.5M=0s
2023-09-28 15:23:33 (70.5 MB/s) - ‘GSE121810_series_matrix.txt.gz’ saved [3326/3326]
Quitting from lines 178-201 [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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nebbiolo2 Summary
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| Package: SurfR |
| Version: 0.99.12 |
| 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 40.74 seconds |
| CheckCommand: BiocCheckGitClone('SurfR') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3105/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3105/ba5e0a2787ae9df5f1c23ca00a5750964bea4c59/SurfR.install-out.txt SurfR_0.99.12.tar.gz && BiocCheck('SurfR_0.99.12.tar.gz', `new-package`=TRUE) |
| CheckTime: 7 minutes 10.47 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 180.78 KiB |
| BuildID:: SurfR_20230928191933 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SurfR. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 1. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking 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 ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘SurfR/data/ind_deg.rda’
* building ‘SurfR_0.99.12.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('SurfR')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: SurfR
─ PackageVersion: 0.99.12
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3105/ba5e0a2787ae9df5f1c23ca00a5750964bea4c59/SurfR
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3105/ba5e0a2787ae9df5f1c23ca00a5750964bea4c59/SurfR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SurfR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SurfR’ version ‘0.99.12’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SurfR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [39s/39s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [92s/131s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TCGA_download 17.770 0.261 12.101
Gene2SProtein 15.296 0.859 16.158
Annotate_SPID 12.060 1.208 31.934
Splot 6.812 0.248 7.059
DownloadArchS4 1.300 0.163 21.513
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [32s/32s]
[32s/32s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: OK
===============================
BiocCheck('SurfR_0.99.12.tar.gz')
===============================
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3105/ba5e0a2787ae9df5f1c23ca00a5750964bea4c59/SurfR_0.99.12.tar.gz
must be installable.
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3105/ba5e0a2787ae9df5f1c23ca00a5750964bea4c59/SurfR_0.99.12.tar.gz
must be loadable.
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: SurfR
─ PackageVersion: 0.99.12
─ sourceDir: /tmp/RtmpXGtIGF/file1a12790e7be7/SurfR
─ installDir: /tmp/RtmpXGtIGF/file1a1276a415610
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3105/ba5e0a2787ae9df5f1c23ca00a5750964bea4c59/SurfR.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 3.5.0 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
no package 'SurfR' was found
Error in pkg_desc$Imports : $ operator is invalid for atomic vectors
Calls: BiocCheck ... checkDescriptionNamespaceConsistency -> cleanupDependency
Execution halted
nebbiolo2 BUILD BIN output
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