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