Last updated on 2018-09-23 07:47:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 20.21 | 286.95 | 307.16 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 15.48 | 222.45 | 237.93 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 349.23 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 350.71 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0.0 | 49.00 | 365.00 | 414.00 | OK | |
| r-patched-linux-x86_64 | 1.0.0 | 13.75 | 237.11 | 250.86 | OK | |
| r-patched-solaris-x86 | 1.0.0 | 417.90 | NOTE | |||
| r-release-linux-x86_64 | 1.0.0 | 14.33 | 237.77 | 252.10 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.0 | 29.00 | 341.00 | 370.00 | OK | |
| r-release-osx-x86_64 | 1.0.0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.0 | 30.00 | 390.00 | 420.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.0 | NOTE |
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’ [43s/47s]
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/RtmpBM9O20/file5b904d83ef05 /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/RtmpBM9O20/file5b9045ade478 -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 [2018-09-20 12:21:38] 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’ [42s/47s]
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/Rtmp1Js8k1/file3e5f437963b7 /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/Rtmp1Js8k1/file3e5f6520a609 -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 [2018-09-17 16:40:14] 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: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Hs.eg.db’
Flavor: r-oldrel-osx-x86_64