CRAN Package Check Results for Package annovarR

Last updated on 2018-08-20 07:47:30 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 15.22 281.59 296.81 OK
r-devel-linux-x86_64-debian-gcc 1.0.0 16.14 220.88 237.02 OK
r-devel-linux-x86_64-fedora-clang 1.0.0 343.83 ERROR
r-devel-linux-x86_64-fedora-gcc 1.0.0 347.84 ERROR
r-devel-windows-ix86+x86_64 1.0.0 53.00 365.00 418.00 ERROR
r-patched-linux-x86_64 1.0.0 15.42 236.23 251.65 OK
r-patched-solaris-x86 1.0.0 425.20 NOTE
r-release-linux-x86_64 1.0.0 14.42 237.38 251.80 OK
r-release-windows-ix86+x86_64 1.0.0 64.00 305.00 369.00 OK
r-release-osx-x86_64 1.0.0 OK
r-oldrel-windows-ix86+x86_64 1.0.0 24.00 302.00 326.00 OK
r-oldrel-osx-x86_64 1.0.0 NOTE

Check Details

Version: 1.0.0
Check: installed package size
Result: NOTE
     installed size is 5.0Mb
     sub-directories of 1Mb or more:
     extdata 4.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86

Version: 1.0.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [42s/46s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(DBI)
     > library(annovarR)
     >
     >
     > test_check("annovarR")
     OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
     OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
     /usr/bin/perl /opt/bin/annovar/table_annovar.pl /tmp/RtmpJss8Zu/file7db025dbfd2e /opt/bin/annovar/humandb -buildver hg19 -remove -protocol refGene -operation g -nastring NA
     /usr/bin/perl /opt/bin/annovar//table_annovar.pl /tmp/test.vcf /opt/bin/annovar//humandb -buildver hg19 -out /tmp/RtmpJss8Zu/file7db02823f149 -remove -protocol ensGene -operation g -nastring NA -vcfinput
     trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
     Content type 'text/plain; charset=utf-8' length 3131 bytes
     ==================================================
     downloaded 3131 bytes
    
     perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -downdb -buildver hg19 -webfrom annovar avsnp147 /data/gannet/ripley/tmp/annovar.dir/humandb
     perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -buildver hg19 /data/gannet/ripley/tmp/annovar.dir/humandb
     perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -regionanno -buildver hg19 -dbtype cytoBand /data/gannet/ripley/tmp/annovar.dir/humandb
     perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -filter -buildver hg19 -dbtype avsnp147 /data/gannet/ripley/tmp/annovar.dir/humandb
     perl /data/gannet/ripley/tmp/annovar.dir/table_annovar.pl example.avinput /data/gannet/ripley/tmp/annovar.dir/humandb -buildver hg19 -remove -protocol refGene,cytoBand,avsnp147 -operation g,r,f -nastring NA
     perl /data/gannet/ripley/tmp/annovar.dir/convert2annovar.pl -format vcf4old example.vcf > example.avinput
     vep --cache_version 91 --assembly GRCh37 --dir /data/gannet/ripley/.vep --output_file variant_effect_output.txt --cache --offline --everything
     vcfanno_linux64 -p 2 /data/gannet/ripley/R/packages/tests-clang/annovarR.Rcheck/annovarR/extdata/demo/vcfanno_demo/conf.toml input.vcf > output.vcf
     ── 1. Error: select.dat.full.match (@test_utils.R#22) ─────────────────────────
     Failed to connect to database: Unknown database 'annovarr'
     1: dbConnect(RMySQL::MySQL(), dbname = "annovarr") at testthat/test_utils.R:22
     2: dbConnect(RMySQL::MySQL(), dbname = "annovarr")
     3: .local(drv, ...)
    
     INFO [2018-08-15 22:45:29] info.msg
     [1] "print.vb"
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 93 SKIPPED: 0 FAILED: 1
     1. Error: select.dat.full.match (@test_utils.R#22)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [45s/96s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(DBI)
     > library(annovarR)
     >
     >
     > test_check("annovarR")
     /usr/bin/perl /opt/bin/annovar/table_annovar.pl /tmp/RtmpfcisCM/file9246386276d8 /opt/bin/annovar/humandb -buildver hg19 -remove -protocol refGene -operation g -nastring NA
     /usr/bin/perl /opt/bin/annovar//table_annovar.pl /tmp/test.vcf /opt/bin/annovar//humandb -buildver hg19 -out /tmp/RtmpfcisCM/file9246594e4935 -remove -protocol ensGene -operation g -nastring NA -vcfinput
     trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
     Content type 'text/plain; charset=utf-8' length 3131 bytes
     ==================================================
     downloaded 3131 bytes
    
     perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -downdb -buildver hg19 -webfrom annovar avsnp147 /data/gannet/ripley/tmp/annovar.dir/humandb
     perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -buildver hg19 /data/gannet/ripley/tmp/annovar.dir/humandb
     perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -regionanno -buildver hg19 -dbtype cytoBand /data/gannet/ripley/tmp/annovar.dir/humandb
     perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -filter -buildver hg19 -dbtype avsnp147 /data/gannet/ripley/tmp/annovar.dir/humandb
     perl /data/gannet/ripley/tmp/annovar.dir/table_annovar.pl example.avinput /data/gannet/ripley/tmp/annovar.dir/humandb -buildver hg19 -remove -protocol refGene,cytoBand,avsnp147 -operation g,r,f -nastring NA
     perl /data/gannet/ripley/tmp/annovar.dir/convert2annovar.pl -format vcf4old example.vcf > example.avinput
     vep --cache_version 91 --assembly GRCh37 --dir /data/gannet/ripley/.vep --output_file variant_effect_output.txt --cache --offline --everything
     vcfanno_linux64 -p 2 /data/gannet/ripley/R/packages/tests-devel/annovarR.Rcheck/annovarR/extdata/demo/vcfanno_demo/conf.toml input.vcf > output.vcf
     ── 1. Error: select.dat.full.match (@test_utils.R#22) ─────────────────────────
     Failed to connect to database: Unknown database 'annovarr'
     1: dbConnect(RMySQL::MySQL(), dbname = "annovarr") at testthat/test_utils.R:22
     2: dbConnect(RMySQL::MySQL(), dbname = "annovarr")
     3: .local(drv, ...)
    
     INFO [2018-08-16 19:52:56] info.msg
     [1] "print.vb"
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 93 SKIPPED: 0 FAILED: 1
     1. Error: select.dat.full.match (@test_utils.R#22)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.0
Check: tests
Result: ERROR
     Running 'testthat.R' [48s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(DBI)
     > library(annovarR)
     >
     >
     > test_check("annovarR")
     D:\Compiler\perl-basic\bin\perl.exe d:\opt\bin\annovar\table_annovar.pl D:\temp\Rtmpm2y0ki\file2a440552b4eb6 d:\opt\bin\annovar\humandb -buildver hg19 -remove -protocol refGene -operation g -nastring NA
     D:\Compiler\perl-basic\bin\perl.exe d:\opt\bin\annovar\table_annovar.pl d:\tmp\test.vcf d:\opt\bin\annovar\humandb -buildver hg19 -out D:\temp\Rtmpm2y0ki\file2a4403f7a351f -remove -protocol ensGene -operation g -nastring NA -vcfinput
     trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
     -- 1. Failure: download.database (@test_download.R#9) -------------------------
     `x` not equal to `expected`.
     1 element mismatch
    
     -- 2. Failure: download.database (@test_download.R#12) ------------------------
     `x` not equal to `expected`.
     1 element mismatch
    
     -- 3. Failure: download.database (@test_download.R#14) ------------------------
     `x` not equal to `expected`.
     'is.NA' value mismatch: 0 in current 1 in target
    
     d:\Rcompile\CRANpkg\local\3.6\annovarR.Rcheck\tests\testthat\perl C:\Users\CRAN\Documents\tmp\annovar.dir\annotate_variation.pl -downdb -buildver hg19 -webfrom annovar avsnp147 C:\Users\CRAN\Documents\tmp\annovar.dir\humandb
     d:\Rcompile\CRANpkg\local\3.6\annovarR.Rcheck\tests\testthat\perl C:\Users\CRAN\Documents\tmp\annovar.dir\annotate_variation.pl -buildver hg19 C:\Users\CRAN\Documents\tmp\annovar.dir\humandb
     d:\Rcompile\CRANpkg\local\3.6\annovarR.Rcheck\tests\testthat\perl C:\Users\CRAN\Documents\tmp\annovar.dir\annotate_variation.pl -regionanno -buildver hg19 -dbtype cytoBand C:\Users\CRAN\Documents\tmp\annovar.dir\humandb
     d:\Rcompile\CRANpkg\local\3.6\annovarR.Rcheck\tests\testthat\perl C:\Users\CRAN\Documents\tmp\annovar.dir\annotate_variation.pl -filter -buildver hg19 -dbtype avsnp147 C:\Users\CRAN\Documents\tmp\annovar.dir\humandb
     d:\Rcompile\CRANpkg\local\3.6\annovarR.Rcheck\tests\testthat\perl C:\Users\CRAN\Documents\tmp\annovar.dir\table_annovar.pl d:\Rcompile\CRANpkg\local\3.6\annovarR.Rcheck\tests\testthat\example.avinput C:\Users\CRAN\Documents\tmp\annovar.dir\humandb -buildver hg19 -remove -protocol refGene,cytoBand,avsnp147 -operation g,r,f -nastring NA
     d:\Rcompile\CRANpkg\local\3.6\annovarR.Rcheck\tests\testthat\perl C:\Users\CRAN\Documents\tmp\annovar.dir\convert2annovar.pl -format vcf4old d:\Rcompile\CRANpkg\local\3.6\annovarR.Rcheck\tests\testthat\example.vcf > d:\Rcompile\CRANpkg\local\3.6\annovarR.Rcheck\tests\testthat\example.avinput
     vep --cache_version 91 --assembly GRCh37 --dir C:\Users\CRAN\Documents/.vep --output_file variant_effect_output.txt --cache --offline --everything
     vcfanno_linux64 -p 2 D:/temp/RtmpgpaAmq/RLIBS_1d75833152983/annovarR/extdata/demo/vcfanno_demo/conf.toml input.vcf > output.vcf
     INFO [2018-08-17 15:00:24] info.msg
     [1] "print.vb"
     == testthat results ===========================================================
     OK: 89 SKIPPED: 0 FAILED: 3
     1. Failure: download.database (@test_download.R#9)
     2. Failure: download.database (@test_download.R#12)
     3. Failure: download.database (@test_download.R#14)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.0.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘org.Hs.eg.db’
Flavor: r-oldrel-osx-x86_64