Yu Sun
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/CrossICC |
| Branch: RELEASE_3_11 |
| Last Commit: 97414a7 |
| Last Changed Date: 2020-04-27 15:30:11 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:23 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE CrossICC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 395/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CrossICC 1.2.0 Yu Sun
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: CrossICC |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrossICC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CrossICC_1.2.0.tar.gz |
| StartedAt: 2020-10-17 03:02:52 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:09:02 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 370.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CrossICC.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrossICC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CrossICC_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CrossICC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CrossICC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CrossICC' version '1.2.0'
* 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 'CrossICC' 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 ... NOTE
.mergemodel: no visible global function definition for 'coxph'
CrossICC: no visible global function definition for '.'
FAIME: no visible binding for global variable 'SampleExp'
get.max.var.rows: no visible binding for global variable 'V1'
predictor: no visible global function definition for 'assay'
runFAIME: no visible global function definition for 'assay'
Undefined global functions or variables:
. SampleExp V1 assay coxph
* 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
summaryCrossICC 20.47 0.09 20.56
CrossICC 19.21 0.25 19.50
predictor 18.62 0.10 18.72
ssGSEA 18.17 0.06 18.23
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
predictor 20.28 0.08 20.31
summaryCrossICC 20.05 0.08 20.15
ssGSEA 19.81 0.09 20.00
CrossICC 18.10 0.12 18.22
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/CrossICC.Rcheck/00check.log'
for details.
CrossICC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CrossICC_1.2.0.tar.gz && rm -rf CrossICC.buildbin-libdir && mkdir CrossICC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CrossICC.buildbin-libdir CrossICC_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CrossICC_1.2.0.zip && rm CrossICC_1.2.0.tar.gz CrossICC_1.2.0.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 2108k 100 2108k 0 0 20.5M 0 --:--:-- --:--:-- --:--:-- 21.9M
install for i386
* installing *source* package 'CrossICC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CrossICC'
finding HTML links ... done
Cal.ARI html
CrossICC html
CrossICCInput html
centroidOfcentroid html
demo.platforms html
get_jarrad_index_df_fromDF html
get_jarrad_index_df_fromlist html
get_overlap_test_by_fisher html
predictor html
rand.index html
ssGSEA html
summaryCrossICC 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 'CrossICC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CrossICC' as CrossICC_1.2.0.zip
* DONE (CrossICC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CrossICC' successfully unpacked and MD5 sums checked
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CrossICC.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(CrossICC)
Loading required package: MASS
>
> test_check("CrossICC")
Sat Oct 17 03:07:09 2020 -- start iteration: 1
352 genes were engaged in this iteration.
Sat Oct 17 03:07:21 2020 -- start iteration: 2
349 genes were engaged in this iteration.
Sat Oct 17 03:07:32 2020 -- start iteration: 3
349 genes were engaged in this iteration.
A CrossICC.object.rds file will be generated in home directory by default.
Note that the previous file will be overridden.
Sat Oct 17 03:07:44 2020 -- Iteration finished! Iteration time for reaching convergence/limit: 2
== testthat results ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
38.1 0.4 38.7
|
CrossICC.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(CrossICC)
Loading required package: MASS
>
> test_check("CrossICC")
Sat Oct 17 03:07:48 2020 -- start iteration: 1
351 genes were engaged in this iteration.
Sat Oct 17 03:08:05 2020 -- start iteration: 2
313 genes were engaged in this iteration.
Sat Oct 17 03:08:18 2020 -- start iteration: 3
312 genes were engaged in this iteration.
Sat Oct 17 03:08:36 2020 -- start iteration: 4
312 genes were engaged in this iteration.
A CrossICC.object.rds file will be generated in home directory by default.
Note that the previous file will be overridden.
Sat Oct 17 03:08:53 2020 -- Iteration finished! Iteration time for reaching convergence/limit: 3
== testthat results ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
67.92 0.50 68.42
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CrossICC.Rcheck/examples_i386/CrossICC-Ex.timings
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CrossICC.Rcheck/examples_x64/CrossICC-Ex.timings
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