'Raik Otto'
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Uniquorn |
| Branch: RELEASE_3_9 |
| Last Commit: 038db65 |
| Last Changed Date: 2019-05-02 11:54:00 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:35:10 -0400 (Wed, 16 Oct 2019).
| Package 1701/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Uniquorn 2.4.0 'Raik Otto'
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Uniquorn |
| Version: 2.4.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Uniquorn.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Uniquorn_2.4.0.tar.gz |
| StartedAt: 2019-10-16 07:46:38 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:52:48 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 370.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Uniquorn.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Uniquorn.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Uniquorn_2.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Uniquorn.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 ... OK
* checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
extdata 6.5Mb
* 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 global function definition for
'fread'
parse_ccle_genotype_data: no visible binding for global variable
'Tumor_Sample_Barcode'
parse_ccle_genotype_data: no visible global function definition for
'data.table'
parse_ccle_genotype_data: no visible binding for global variable '.SD'
parse_ccle_genotype_data: no visible binding for global variable
'Index'
parse_cosmic_genotype_data: no visible global function definition for
'fread'
parse_cosmic_genotype_data: no visible binding for global variable
'position'
parse_cosmic_genotype_data: no visible global function definition for
'data.table'
parse_cosmic_genotype_data: no visible binding for global variable
'.SD'
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:
.SD Index Tumor_Sample_Barcode ccls_all data.table fread
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 3.38 0.56 5.59
** 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Uniquorn_2.4.0.tar.gz && rm -rf Uniquorn.buildbin-libdir && mkdir Uniquorn.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Uniquorn.buildbin-libdir Uniquorn_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Uniquorn_2.4.0.zip && rm Uniquorn_2.4.0.tar.gz Uniquorn_2.4.0.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 2292k 100 2292k 0 0 13.9M 0 --:--:-- --:--:-- --:--:-- 14.6M
install for i386
* installing *source* package 'Uniquorn' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Uniquorn' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Uniquorn' as Uniquorn_2.4.0.zip
* DONE (Uniquorn)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Uniquorn' successfully unpacked and MD5 sums checked
|
Uniquorn.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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")
>
> test_check("Uniquorn")
== testthat results ===========================================================
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
15.10 1.48 16.57
|
Uniquorn.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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")
>
> test_check("Uniquorn")
== testthat results ===========================================================
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
19.39 0.78 20.15
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Uniquorn.Rcheck/examples_i386/Uniquorn-Ex.timings
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Uniquorn.Rcheck/examples_x64/Uniquorn-Ex.timings
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