Claudia Cava
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/SpidermiR |
| Branch: RELEASE_3_11 |
| Last Commit: 7a7eaa7 |
| Last Changed Date: 2020-10-01 11:44:24 -0400 (Thu, 01 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:51 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE SpidermiR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1712/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SpidermiR 1.18.2 Claudia Cava
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: SpidermiR |
| Version: 1.18.2 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpidermiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SpidermiR_1.18.2.tar.gz |
| StartedAt: 2020-10-17 08:32:10 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:44:30 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 740.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SpidermiR.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpidermiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SpidermiR_1.18.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SpidermiR.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 'SpidermiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SpidermiR' version '1.18.2'
* 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 'SpidermiR' can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'simpleNetwork(NetworkData, ': unused argument (textColour = "black")
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SpidermiR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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 ... NOTE
Namespace in Imports field not imported from: 'TCGAbiolinks'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.SpidermiRvisualize_gene: possible error in simpleNetwork(NetworkData,
linkColour = "gray", textColour = "black", zoom = TRUE): unused
argument (textColour = "black")
SpidermiRdownload_pharmacomir: no visible binding for global variable
'drug_gene'
SpidermiRvisualize_plot_target: no visible binding for global variable
'miRNAs'
SpidermiRvisualize_plot_target: no visible binding for global variable
'mRNA_target'
Undefined global functions or variables:
drug_gene mRNA_target miRNAs
* 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 (user + system) or elapsed time > 5s
user system elapsed
SpidermiRquery_disease 27.69 6.42 35.96
SpidermiRdownload_pharmacomir 20.93 0.23 37.41
SpidermiRdownload_drug_gene 19.16 0.16 19.80
SpidermiRprepare_NET 13.12 3.30 16.87
SpidermiRdownload_net 7.28 2.22 9.95
SpidermiRdownload_miRNAextra_cir 4.73 1.57 6.66
SpidermiRdownload_miRNAprediction 4.57 0.44 5.00
SpidermiRdownload_miRNAvalidate 1.09 0.14 18.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SpidermiRquery_disease 23.83 12.10 40.15
SpidermiRdownload_drug_gene 20.32 0.22 21.03
SpidermiRdownload_pharmacomir 16.50 0.29 36.94
SpidermiRprepare_NET 9.30 3.36 13.11
SpidermiRdownload_net 4.06 1.85 6.29
SpidermiRdownload_miRNAprediction 4.97 0.41 5.38
SpidermiRdownload_miRNAvalidate 1.96 0.01 20.13
* 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/SpidermiR.Rcheck/00check.log'
for details.
SpidermiR.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/SpidermiR_1.18.2.tar.gz && rm -rf SpidermiR.buildbin-libdir && mkdir SpidermiR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpidermiR.buildbin-libdir SpidermiR_1.18.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SpidermiR_1.18.2.zip && rm SpidermiR_1.18.2.tar.gz SpidermiR_1.18.2.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 22465 100 22465 0 0 331k 0 --:--:-- --:--:-- --:--:-- 371k
install for i386
* installing *source* package 'SpidermiR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'simpleNetwork(NetworkData, ': unused argument (textColour = "black")
** help
*** installing help indices
converting help for package 'SpidermiR'
finding HTML links ... done
SpidermiRanalyze_Community_detection html
SpidermiRanalyze_Community_detection_bi
html
SpidermiRanalyze_Community_detection_net
html
SpidermiRanalyze_degree_centrality html
SpidermiRanalyze_direct_net html
SpidermiRanalyze_direct_subnetwork html
SpidermiRanalyze_subnetwork_neigh html
SpidermiRdownload_drug_gene html
SpidermiRdownload_miRNAextra_cir html
SpidermiRdownload_miRNAprediction html
SpidermiRdownload_miRNAprediction_mmu html
SpidermiRdownload_miRNAvalidate html
SpidermiRdownload_net html
SpidermiRdownload_pharmacomir html
SpidermiRprepare_NET html
SpidermiRquery_disease html
SpidermiRquery_networks_type html
SpidermiRquery_spec_networks html
SpidermiRquery_species html
SpidermiRvisualize_3Dbarplot html
SpidermiRvisualize_BI html
SpidermiRvisualize_adj_matrix html
SpidermiRvisualize_degree_dist html
SpidermiRvisualize_direction html
SpidermiRvisualize_mirnanet html
SpidermiRvisualize_plot_target 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 'SpidermiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpidermiR' as SpidermiR_1.18.2.zip
* DONE (SpidermiR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SpidermiR' successfully unpacked and MD5 sums checked
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SpidermiR.Rcheck/examples_i386/SpidermiR-Ex.timings
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SpidermiR.Rcheck/examples_x64/SpidermiR-Ex.timings
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