Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/scQTLtools
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 24.04.1 LTS)/x86_64   OK     WARNINGS     skipped     OK  

nebbiolo1 Summary

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Package: scQTLtools
Version: 0.99.3
RVersion: 4.5
BiocVersion: 3.21
BuildCommand: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scQTLtools
BuildTime: 1 minutes 28.11 seconds
CheckCommand: BiocCheckGitClone('scQTLtools') && /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3515/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3515/927f2509fe13f5f36e60a87dba430f5f0198dc2e/scQTLtools.install-out.txt scQTLtools_0.99.3.tar.gz && BiocCheck('scQTLtools_0.99.3.tar.gz', `new-package`=TRUE)
CheckTime: 12 minutes 2.26 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 2209.10 KiB
BuildID:: scQTLtools_20241202032641
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scQTLtools. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.WARNING: check time exceeded 10 min.

nebbiolo1 BUILD SRC output

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 R CMD BUILD

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* checking for file scQTLtools/DESCRIPTION ... OK
* preparing scQTLtools:
* 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
* building scQTLtools_0.99.3.tar.gz


nebbiolo1 CHECK output

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 BiocCheckGitClone('scQTLtools')

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 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3515/927f2509fe13f5f36e60a87dba430f5f0198dc2e/scQTLtools
 BiocVersion: 3.21
 Package: scQTLtools
 PackageVersion: 0.99.3
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3515/927f2509fe13f5f36e60a87dba430f5f0198dc2e/scQTLtools.BiocCheck
 BiocCheckVersion: 1.43.2
 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3515/927f2509fe13f5f36e60a87dba430f5f0198dc2e/scQTLtools
 installDir: NULL
 isTarBall: FALSE
 platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
 BiocCheck v1.43.2 results 
 0 ERRORS |  0 WARNINGS | i 0 NOTES
i For more details, run
  browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3515/927f2509fe13f5f36e60a87dba430f5f0198dc2e/scQTLtools.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file scQTLtools/DESCRIPTION ... OK
* checking extension type ... Package
* this is package scQTLtools version 0.99.3
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 scQTLtools 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [38s/38s] 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 ... [12s/12s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [36s/189s] ERROR
Running examples in scQTLtools-Ex.R failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: createSNPsLoc
> ### Title: Create SNP location dataframe.
> ### Aliases: createSNPsLoc
> 
> ### ** Examples
> 
> snpList <- c('rs546', 'rs549', 'rs568', 'rs665', 'rs672')
> snpDataset <- 'hsapiens_snp'
> snpBiomart <- "ENSEMBL_MART_SNP"
> snp_loc <- createSNPsLoc(snpList = snpList,
+                          snpDataset = snpDataset,
+                          snpBiomart = snpBiomart)
Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
DESeq_normalize 7.653  0.954   8.607
createGeneLoc   1.329  0.028 153.663
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running testthat.R [100s/100s]
 [100s/101s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
   1. scQTLtools::callQTL(eqtl, downstream = -8.5e+07, upstream = 2e+07) at test-callQTL.R:38:3
   2.   scQTLtools:::match_gene_snp(...)
   3.     scQTLtools::createGeneLoc(...)
   4.       biomaRt::useMart(...)
   5.         biomaRt:::.useMart(...)
   6.           biomaRt:::.listMarts(...)
   Error ('test-callQTL.R:74:3'): Function returns correct output with valid SNP matrix rownames 
  Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
  Look at ?useEnsembl for details on how to try a mirror site.
  Backtrace:
      
   1. scQTLtools::callQTL(eqtl, downstream = -1e+06, upstream = 5e+06) at test-callQTL.R:74:3
   2.   scQTLtools:::match_gene_snp(...)
   3.     scQTLtools::checkSNPList(snpList, snpDataset, snpBiomart)
   4.       scQTLtools::createSNPsLoc(snpList, snpDataset, snpBiomart)
   5.         biomaRt::useMart(biomart = snpBiomart, dataset = snpDataset)
   6.           biomaRt:::.useMart(...)
   7.             biomaRt:::.listMarts(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 52 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE

Status: 2 ERRORs
See
  /home/pkgbuild/packagebuilder/workers/jobs/3515/927f2509fe13f5f36e60a87dba430f5f0198dc2e/scQTLtools.Rcheck/00check.log
for details.

 WARNING: R CMD check exceeded 10 min requirement






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 BiocCheck('scQTLtools_0.99.3.tar.gz')

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 Installing scQTLtools 
 Package installed successfully
 scQTLtools session metadata 
 sourceDir: /tmp/RtmpUNHOU6/file3870221d847b93/scQTLtools
 BiocVersion: 3.21
 Package: scQTLtools
 PackageVersion: 0.99.3
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3515/927f2509fe13f5f36e60a87dba430f5f0198dc2e/scQTLtools.BiocCheck
 BiocCheckVersion: 1.43.2
 sourceDir: /tmp/RtmpUNHOU6/file3870221d847b93/scQTLtools
 installDir: /tmp/RtmpUNHOU6/file3870221ed2e11
 isTarBall: TRUE
 platform: unix
 Running BiocCheck on scQTLtools 
* 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...
i NOTE: Update R version dependency from 4.4.1.0 to 4.5.0.
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (11%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scQTLtools...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...

Registered S3 method overwritten by 'gamlss':
  method   from
  print.ri bit 
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
 BiocCheck v1.43.2 results 
 0 ERRORS |  0 WARNINGS | i 1 NOTES
i See the scQTLtools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

nebbiolo1 BUILD BIN output

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