SpidermiR 1.2.2
Claudia Cava
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SpidermiR | | Last Changed Rev: 119921 / Revision: 121152 | | Last Changed Date: 2016-08-06 04:13:18 -0700 (Sat, 06 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf SpidermiR.buildbin-libdir SpidermiR.Rcheck && mkdir SpidermiR.buildbin-libdir SpidermiR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpidermiR.buildbin-libdir SpidermiR_1.2.2.tar.gz >SpidermiR.Rcheck\00install.out 2>&1 && cp SpidermiR.Rcheck\00install.out SpidermiR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SpidermiR.buildbin-libdir --install="check:SpidermiR-install.out" --force-multiarch --no-vignettes --timings SpidermiR_1.2.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/SpidermiR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.2.2'
* 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 ... 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
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:
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'SpidermiR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpidermiRanalyze_DEnetworkTCGA
> ### Title: Integration with TCGA data in order to obtain a network of
> ### differentially expressed (DE) genes or miRNAs.
> ### Aliases: SpidermiRanalyze_DEnetworkTCGA
>
> ### ** Examples
>
> devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")
Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master
Installing TCGAbiolinks
"D:/biocbld/BBS-3˜1.4-B/R/bin/i386/R" --no-site-file --no-environ --no-save \
--no-restore --quiet CMD INSTALL \
"D:/biocbld/bbs-3.4-bioc/tmpdir/Rtmp4YZ65U/devtools1ce03cd72e4c/BioinformaticsFMRP-TCGAbiolinks-2fcc8de" \
--library="D:/biocbld/bbs-3.4-bioc/meat/SpidermiR.buildbin-libdir" \
--install-tests
* installing *source* package 'TCGAbiolinks' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (TCGAbiolinks)
> library(TCGAbiolinks)
> miRNA_cN <-data.frame(gA=c('hsa-let-7a','SSTR1'),gB=c('FOXM1','GATA5'),stringsAsFactors=FALSE)
> cancer <- "TCGA-BRCA"
> PlatformCancer <- "Illumina HiSeq"
> tumour<-c("TCGA-BH-A0DL-01A-11R-A115-07","TCGA-AO-A03P-01A-11R-A00Z-07")
> normal<-c("TCGA-BH-A209-11A-42R-A157-07","TCGA-E9-A1N4-11A-33R-A14M-07")
> de_int<-SpidermiRanalyze_DEnetworkTCGA(data=miRNA_cN,
+ cancer,
+ PlatformCancer,
+ tumour,
+ normal,
+ path = "exampleData")
Error in open.connection(con, "rb") :
Failure when receiving data from the peer
Calls: SpidermiRanalyze_DEnetworkTCGA ... fromJSON_string -> parseJSON -> parse_con -> open -> open.connection
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'SpidermiR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpidermiRanalyze_DEnetworkTCGA
> ### Title: Integration with TCGA data in order to obtain a network of
> ### differentially expressed (DE) genes or miRNAs.
> ### Aliases: SpidermiRanalyze_DEnetworkTCGA
>
> ### ** Examples
>
> devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")
Skipping install of 'TCGAbiolinks' from a github remote, the SHA1 (2fcc8dec) has not changed since last install.
Use `force = TRUE` to force installation
> library(TCGAbiolinks)
> miRNA_cN <-data.frame(gA=c('hsa-let-7a','SSTR1'),gB=c('FOXM1','GATA5'),stringsAsFactors=FALSE)
> cancer <- "TCGA-BRCA"
> PlatformCancer <- "Illumina HiSeq"
> tumour<-c("TCGA-BH-A0DL-01A-11R-A115-07","TCGA-AO-A03P-01A-11R-A00Z-07")
> normal<-c("TCGA-BH-A209-11A-42R-A157-07","TCGA-E9-A1N4-11A-33R-A14M-07")
> de_int<-SpidermiRanalyze_DEnetworkTCGA(data=miRNA_cN,
+ cancer,
+ PlatformCancer,
+ tumour,
+ normal,
+ path = "exampleData")
Error in open.connection(con, "rb") :
Failure when receiving data from the peer
Calls: SpidermiRanalyze_DEnetworkTCGA ... fromJSON_string -> parseJSON -> parse_con -> open -> open.connection
Execution halted
* 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 ERRORs, 1 NOTE
See
'D:/biocbld/bbs-3.4-bioc/meat/SpidermiR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'SpidermiR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'SpidermiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpidermiR' as SpidermiR_1.2.2.zip
* DONE (SpidermiR)