'Raik Otto'
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Uniquorn |
| Branch: RELEASE_3_8 |
| Last Commit: 9a1b9e4 |
| Last Changed Date: 2019-01-04 13:08:11 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:25 -0400 (Sat, 13 Apr 2019).
| Package 1612/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Uniquorn 2.2.1 'Raik Otto'
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: Uniquorn |
| Version: 2.2.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Uniquorn.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Uniquorn_2.2.1.tar.gz |
| StartedAt: 2019-04-13 06:07:46 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 06:13:46 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 360.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Uniquorn.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Uniquorn.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Uniquorn_2.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Uniquorn.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Uniquorn/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Uniquorn' version '2.2.1'
* 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 whether package 'Uniquorn' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn'
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Uniquorn.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
extdata 4.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
add_p_q_values_statistics: no visible binding for '<<-' assignment to
'sig_vec'
add_p_q_values_statistics: no visible binding for global variable
'sig_vec'
create_bed_file: no visible binding for global variable 'res_table'
create_bed_file: no visible binding for global variable 'sim_list'
identify_vcf_file: no visible binding for global variable
'vcf_fingerprint'
identify_vcf_file: no visible binding for global variable
'output_file_xls'
init_and_load_identification: no visible global function definition for
'tail'
parse_ccle_genotype_data: no visible binding for global variable
'Tumor_Sample_Barcode'
parse_ccle_genotype_data: no visible binding for global variable
'Index'
parse_cosmic_genotype_data: no visible binding for global variable
'position'
parse_cosmic_genotype_data: no visible binding for global variable
'Index'
show_contained_ccls: no visible binding for '<<-' assignment to
'ccls_all'
show_contained_ccls: no visible binding for global variable 'ccls_all'
write_w0_and_split_w0_into_lower_weights: no visible binding for '<<-'
assignment to 'g_mat_exclude'
write_w0_and_split_w0_into_lower_weights: no visible binding for global
variable 'g_mat_exclude'
Undefined global functions or variables:
Index Tumor_Sample_Barcode ccls_all g_mat_exclude output_file_xls
position res_table sig_vec sim_list tail vcf_fingerprint
Consider adding
importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
add_custom_vcf_to_database 3.64 0.36 5.56
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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 ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/Uniquorn.Rcheck/00check.log'
for details.
Uniquorn.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Uniquorn_2.2.1.tar.gz && rm -rf Uniquorn.buildbin-libdir && mkdir Uniquorn.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Uniquorn.buildbin-libdir Uniquorn_2.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Uniquorn_2.2.1.zip && rm Uniquorn_2.2.1.tar.gz Uniquorn_2.2.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2330k 100 2330k 0 0 32.9M 0 --:--:-- --:--:-- --:--:-- 35.0M
install for i386
* installing *source* package 'Uniquorn' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn'
** help
*** installing help indices
converting help for package 'Uniquorn'
finding HTML links ... done
add_custom_vcf_to_database html
add_missing_cls html
add_p_q_values_statistics html
add_penalty_statistics html
create_bed_file html
identify_vcf_file html
init_and_load_identification html
initiate_canonical_databases html
match_query_ccl_to_database html
parse_ccle_genotype_data html
parse_cosmic_genotype_data html
parse_vcf_file html
parse_vcf_query_into_db html
read_library_names html
read_mutation_grange_objects html
remove_ccls_from_database html
remove_library_from_database html
show_contained_ccls html
show_contained_variants_for_ccl html
show_contained_variants_in_library html
show_which_ccls_contain_variant html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn'
In R CMD INSTALL
install for x64
* installing *source* package 'Uniquorn' ...
** testing if installed package can be loaded
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn'
* MD5 sums
packaged installation of 'Uniquorn' as Uniquorn_2.2.1.zip
* DONE (Uniquorn)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Uniquorn' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
Uniquorn.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv(R_TESTS="")
> library("testthat")
> library("Uniquorn")
Warning message:
replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn'
>
> test_check("Uniquorn")
== testthat results ===========================================================
OK: 21 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
13.40 1.57 14.95
|
Uniquorn.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv(R_TESTS="")
> library("testthat")
> library("Uniquorn")
Warning message:
replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn'
>
> test_check("Uniquorn")
== testthat results ===========================================================
OK: 21 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
14.85 0.56 15.42
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Uniquorn.Rcheck/examples_i386/Uniquorn-Ex.timings
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Uniquorn.Rcheck/examples_x64/Uniquorn-Ex.timings
|