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CHECK report for celaref on tokay1

This page was generated on 2019-04-13 11:29:34 -0400 (Sat, 13 Apr 2019).

Package 213/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
celaref 1.0.1
Sarah Williams
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/celaref
Branch: RELEASE_3_8
Last Commit: 5e4a446
Last Changed Date: 2019-01-04 13:24:34 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: celaref
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:celaref.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings celaref_1.0.1.tar.gz
StartedAt: 2019-04-13 01:02:43 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:07:37 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 294.2 seconds
RetCode: 0
Status:  OK  
CheckDir: celaref.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:celaref.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings celaref_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/celaref.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 'celaref/DESCRIPTION' ... OK
* this is package 'celaref' version '1.0.1'
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'celaref' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
contrast_each_group_to_the_rest 21.36   0.48   21.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
contrast_each_group_to_the_rest 26.34   0.11   26.39
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/celaref.Rcheck/00check.log'
for details.



Installation output

celaref.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/celaref_1.0.1.tar.gz && rm -rf celaref.buildbin-libdir && mkdir celaref.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=celaref.buildbin-libdir celaref_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL celaref_1.0.1.zip && rm celaref_1.0.1.tar.gz celaref_1.0.1.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 1694k  100 1694k    0     0  2514k      0 --:--:-- --:--:-- --:--:-- 2529k

install for i386

* installing *source* package 'celaref' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'celaref'
    finding HTML links ... done
    contrast_each_group_to_the_rest         html  
    contrast_each_group_to_the_rest_for_norm_ma_with_limma
                                            html  
    contrast_the_group_to_the_rest          html  
    contrast_the_group_to_the_rest_with_limma_for_microarray
                                            html  
    convert_se_gene_ids                     html  
    de_table.demo_query                     html  
    de_table.demo_ref                       html  
    demo_cell_info_table                    html  
    demo_counts_matrix                      html  
    demo_gene_info_table                    html  
    demo_microarray_expr                    html  
    demo_microarray_sample_sheet            html  
    demo_query_se                           html  
    demo_ref_se                             html  
    find_within_match_differences           html  
    get_inner_or_outer_ci                   html  
    get_limma_top_table_with_ci             html  
    get_matched_stepped_mwtest_res_table    html  
    get_ranking_and_test_results            html  
    get_rankstat_table                      html  
    get_reciprocal_matches                  html  
    get_stepped_pvals_str                   html  
    get_the_up_genes_for_all_possible_groups
                                            html  
    get_the_up_genes_for_group              html  
    get_vs_random_pval                      html  
    load_dataset_10Xdata                    html  
    load_se_from_tables                     html  
    make_ranking_violin_plot                html  
    make_ref_similarity_names               html  
    make_ref_similarity_names_for_group     html  
    run_pair_test_stats                     html  
    trim_small_groups_and_low_expression_genes
                                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'celaref' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'celaref' as celaref_1.0.1.zip
* DONE (celaref)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'celaref' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

celaref.Rcheck/examples_i386/celaref-Ex.timings

nameusersystemelapsed
contrast_each_group_to_the_rest21.36 0.4821.73
contrast_each_group_to_the_rest_for_norm_ma_with_limma0.520.020.56
convert_se_gene_ids0.080.000.08
get_rankstat_table0.040.000.05
get_the_up_genes_for_all_possible_groups000
get_the_up_genes_for_group000
load_dataset_10Xdata0.100.060.34
load_se_from_tables0.210.030.42
make_ranking_violin_plot1.880.071.94
make_ref_similarity_names1.80.01.8
trim_small_groups_and_low_expression_genes0.060.000.06

celaref.Rcheck/examples_x64/celaref-Ex.timings

nameusersystemelapsed
contrast_each_group_to_the_rest26.34 0.1126.39
contrast_each_group_to_the_rest_for_norm_ma_with_limma0.390.040.44
convert_se_gene_ids0.060.000.07
get_rankstat_table0.030.000.03
get_the_up_genes_for_all_possible_groups000
get_the_up_genes_for_group0.020.000.02
load_dataset_10Xdata0.070.030.11
load_se_from_tables0.140.030.17
make_ranking_violin_plot2.600.032.62
make_ref_similarity_names2.340.002.35
trim_small_groups_and_low_expression_genes0.060.000.06