Markus List
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/SPONGE |
| Branch: RELEASE_3_12 |
| Last Commit: 33265cf |
| Last Changed Date: 2020-10-27 11:26:57 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:45 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the SPONGE package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1777/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SPONGE 1.12.0 (landing page) Markus List
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SPONGE |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPONGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SPONGE_1.12.0.tar.gz |
| StartedAt: 2021-05-06 07:14:20 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:22:31 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 491.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SPONGE.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPONGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SPONGE_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SPONGE.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SPONGE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SPONGE' version '1.12.0'
* 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 'SPONGE' can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.3Mb
sub-directories of 1Mb or more:
data 8.0Mb
* 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 ... NOTE
checkLambda: no visible binding for global variable 'i'
check_and_convert_expression_data: no visible global function
definition for 'is'
check_and_convert_expression_data: no visible global function
definition for 'attach.big.matrix'
check_and_convert_expression_data: no visible global function
definition for 'mwhich'
compute_p_values: no visible binding for global variable 'cor_cut'
compute_p_values: no visible binding for global variable 'df_cut'
compute_p_values: no visible global function definition for 'J'
compute_p_values: no visible binding for global variable '.I'
compute_p_values: no visible binding for global variable '.EACHI'
compute_p_values: no visible binding for global variable 'p.val'
compute_p_values: no visible global function definition for ':='
compute_p_values: no visible binding for global variable 'p.adj'
determine_cutoffs_for_null_model_partitioning: no visible global
function definition for ':='
determine_cutoffs_for_null_model_partitioning: no visible binding for
global variable 'cor_cut'
determine_cutoffs_for_null_model_partitioning: no visible binding for
global variable 'df_cut'
fn_elasticnet: no visible binding for global variable 'alpha'
fn_gene_miRNA_F_test: no visible binding for global variable 'mirna'
fn_get_model_coef: no visible binding for global variable 'gene'
isplitDT2 : nextEl: no visible global function definition for '.'
processChunk: no visible binding for global variable 'geneA_idx'
processChunk: no visible binding for global variable 'geneB_idx'
processChunk: no visible binding for global variable 'geneA'
processChunk: no visible binding for global variable 'geneB'
processChunk: no visible binding for global variable 'mirna'
sample_zero_mscor_cov: no visible binding for global variable
'solution'
sample_zero_mscor_cov: no visible global function definition for 'ginv'
sample_zero_mscor_cov: no visible binding for global variable 'i'
sample_zero_mscor_data: no visible binding for global variable
'cov.matrix'
sponge: no visible global function definition for 'is'
sponge: no visible binding for global variable 'i'
sponge: no visible global function definition for 'attach.big.matrix'
sponge: no visible binding for global variable 'gene_combis'
sponge_build_null_model: no visible binding for global variable
'precomputed_cov_matrices'
sponge_build_null_model: no visible binding for global variable
'cov.matrices.m'
sponge_build_null_model: no visible binding for global variable
'cov.matrices.k'
sponge_build_null_model: no visible binding for global variable 'm'
sponge_build_null_model: no visible binding for global variable 'k'
sponge_compute_p_values: no visible binding for global variable 'dt.m'
sponge_compute_p_values: no visible global function definition for ':='
sponge_compute_p_values: no visible binding for global variable
'cor_cut'
sponge_compute_p_values: no visible binding for global variable
'df_cut'
sponge_gene_miRNA_interaction_filter: no visible global function
definition for 'is'
sponge_gene_miRNA_interaction_filter: no visible binding for global
variable 'chunk'
sponge_gene_miRNA_interaction_filter: no visible binding for global
variable 'g_expr_batch'
sponge_gene_miRNA_interaction_filter : <anonymous>: no visible binding
for global variable 'g_expr_batch'
sponge_gene_miRNA_interaction_filter: no visible binding for global
variable 'gene'
sponge_gene_miRNA_interaction_filter: no visible binding for global
variable 'g_expr'
sponge_network: no visible binding for global variable 'gene'
sponge_network: no visible binding for global variable 'mir'
sponge_plot_network_centralities: no visible global function definition
for 'head'
sponge_plot_simulation_results: no visible binding for global variable
'mscor'
sponge_run_benchmark: no visible binding for global variable
'precomputed_cov_matrices'
sponge_run_benchmark: no visible binding for global variable
'elastic.net'
sponge_run_benchmark: no visible binding for global variable
'each.miRNA'
sponge_subsampling: no visible binding for global variable 'sub.n'
sponge_subsampling: no visible binding for global variable 'geneA'
sponge_subsampling: no visible binding for global variable 'geneB'
Undefined global functions or variables:
. .EACHI .I := J alpha attach.big.matrix chunk cor_cut cov.matrices.k
cov.matrices.m cov.matrix df_cut dt.m each.miRNA elastic.net g_expr
g_expr_batch gene geneA geneA_idx geneB geneB_idx gene_combis ginv
head i is k m mir mirna mscor mwhich p.adj p.val
precomputed_cov_matrices solution sub.n
Consider adding
importFrom("methods", "is")
importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 (user + system) or elapsed time > 5s
user system elapsed
sponge_gene_miRNA_interaction_filter 33.08 0.14 33.21
sponge_build_null_model 18.52 0.05 18.56
sponge_run_benchmark 10.54 0.00 10.55
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sponge_gene_miRNA_interaction_filter 44.42 0.10 44.68
sponge_build_null_model 28.37 0.01 28.76
sponge_run_benchmark 15.19 0.00 15.19
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/SPONGE.Rcheck/00check.log'
for details.
SPONGE.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SPONGE_1.12.0.tar.gz && rm -rf SPONGE.buildbin-libdir && mkdir SPONGE.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SPONGE.buildbin-libdir SPONGE_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SPONGE_1.12.0.zip && rm SPONGE_1.12.0.tar.gz SPONGE_1.12.0.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 4103k 100 4103k 0 0 73.3M 0 --:--:-- --:--:-- --:--:-- 74.2M
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'SPONGE/vignettes/SPONGE.Rmd' to 'SPONGE/README.md'
* installing *source* package 'SPONGE' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SPONGE'
finding HTML links ... done
ceRNA_interactions html
check_and_convert_expression_data html
fn_elasticnet html
fn_gene_miRNA_F_test html
fn_get_model_coef html
fn_get_rss html
fn_get_shared_miRNAs html
gene_expr html
genes_pairwise_combinations html
mir_expr html
mir_interactions html
mircode_ensg html
mircode_symbol html
precomputed_cov_matrices html
precomputed_null_model html
sample_zero_mscor_cov html
sample_zero_mscor_data html
sponge html
sponge_build_null_model html
sponge_compute_p_values html
sponge_edge_centralities html
sponge_gene_miRNA_interaction_filter html
sponge_network html
sponge_node_centralities html
sponge_plot_network html
sponge_plot_network_centralities html
sponge_plot_simulation_results html
sponge_run_benchmark html
sponge_subsampling html
targetscan_ensg html
targetscan_symbol 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
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'SPONGE/vignettes/SPONGE.Rmd' to 'SPONGE/README.md'
* installing *source* package 'SPONGE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SPONGE' as SPONGE_1.12.0.zip
* DONE (SPONGE)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SPONGE' successfully unpacked and MD5 sums checked
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SPONGE.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> library(testthat)
> library(SPONGE)
>
> test_check("SPONGE")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 163 ]
>
> proc.time()
user system elapsed
76.37 0.85 93.62
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SPONGE.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> library(testthat)
> library(SPONGE)
>
> test_check("SPONGE")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 163 ]
>
> proc.time()
user system elapsed
96.73 0.54 112.23
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SPONGE.Rcheck/examples_i386/SPONGE-Ex.timings
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SPONGE.Rcheck/examples_x64/SPONGE-Ex.timings
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