Irina Ostrovnaya
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Clonality |
| Branch: RELEASE_3_10 |
| Last Commit: 681c6d1 |
| Last Changed Date: 2019-10-29 13:08:18 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:19:37 -0400 (Wed, 15 Apr 2020).
| Package 302/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Clonality 1.34.0 Irina Ostrovnaya
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Clonality |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Clonality.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Clonality_1.34.0.tar.gz |
| StartedAt: 2020-04-15 02:07:10 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:12:08 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 298.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Clonality.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Clonality.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Clonality_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Clonality.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Clonality/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clonality' version '1.34.0'
* 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 'Clonality' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Foreign function call to a different package:
.Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
get.mutation.frequencies: no visible binding for global variable
'freqdata'
Undefined global functions or variables:
freqdata
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clonality.analysis 69.08 0.33 69.41
LRtesting3or4tumors 28.74 0.00 28.74
LOHclonality 9.07 0.00 9.06
ECMtesting 6.07 0.00 6.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clonality.analysis 73.81 0.23 74.04
LRtesting3or4tumors 23.37 0.00 23.38
LOHclonality 8.06 0.00 8.07
ECMtesting 7.50 0.01 7.51
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/Clonality.Rcheck/00check.log'
for details.
Clonality.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Clonality_1.34.0.tar.gz && rm -rf Clonality.buildbin-libdir && mkdir Clonality.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Clonality.buildbin-libdir Clonality_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Clonality_1.34.0.zip && rm Clonality_1.34.0.tar.gz Clonality_1.34.0.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 2436k 100 2436k 0 0 10.9M 0 --:--:-- --:--:-- --:--:-- 11.1M
install for i386
* installing *source* package 'Clonality' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Clonality'
finding HTML links ... done
Clonality-internal html
Clonality-package html
ECMtesting html
LOHclonality html
LRtesting3or4tumors html
SNVtest html
SNVtest2 html
ave.adj.probes html
chromosomePlots html
clonEM html
clonality.analysis html
create.mutation.matrix html
freqdata html
genomewidePlots html
get.mutation.frequencies html
grid.lik html
histogramPlot html
lcis html
model.lik html
mutation.proba html
mutation.rem html
print.mutation.proba html
print.mutation.rem html
splitChromosomes html
xidens html
** building package indices
** installing vignettes
'Clonality.Rnw'
** 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 'Clonality' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Clonality' as Clonality_1.34.0.zip
* DONE (Clonality)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Clonality' successfully unpacked and MD5 sums checked
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Clonality.Rcheck/examples_i386/Clonality-Ex.timings
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Clonality.Rcheck/examples_x64/Clonality-Ex.timings
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