P.M.V. Rancoita
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/mBPCR |
| Branch: RELEASE_3_10 |
| Last Commit: fcd072c |
| Last Changed Date: 2019-10-29 13:08:06 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:18:56 -0400 (Wed, 15 Apr 2020).
| Package 970/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mBPCR 1.40.0 P.M.V. Rancoita
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: mBPCR |
| Version: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mBPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings mBPCR_1.40.0.tar.gz |
| StartedAt: 2020-04-15 04:30:32 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:34:47 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 255.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mBPCR.Rcheck |
| Warnings: 1 |
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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:mBPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings mBPCR_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/mBPCR.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 'mBPCR/DESCRIPTION' ... OK
* this is package 'mBPCR' version '1.40.0'
* 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 'mBPCR' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'SNPchip' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/mBPCR.Rcheck/00install.out' for details.
* 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 ... OK
* checking R code for possible problems ... NOTE
estProfileWithMBPCRforOligoSnpSet: no visible global function
definition for 'new'
estProfileWithMBPCRforOligoSnpSet: no visible global function
definition for 'integerMatrix'
importCNData: no visible global function definition for 'read.table'
plotEstProfile: no visible global function definition for 'x11'
plotEstProfile: no visible global function definition for 'plot'
plotEstProfile: no visible global function definition for 'title'
plotEstProfile: no visible global function definition for 'legend'
plotEstProfile: no visible global function definition for 'points'
writeEstProfile: no visible global function definition for
'write.table'
Undefined global functions or variables:
integerMatrix legend new plot points read.table title write.table x11
Consider adding
importFrom("grDevices", "x11")
importFrom("graphics", "legend", "plot", "points", "title")
importFrom("methods", "new")
importFrom("utils", "read.table", "write.table")
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 or elapsed time > 5s
user system elapsed
plotEstProfile 12.69 0.09 12.78
estProfileWithMBPCR 5.80 0.17 5.98
writeEstProfile 5.75 0.05 5.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotEstProfile 10.35 0.01 10.36
estProfileWithMBPCR 5.39 0.02 5.41
writeEstProfile 5.15 0.00 5.15
* 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-3.10-bioc/meat/mBPCR.Rcheck/00check.log'
for details.
mBPCR.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/mBPCR_1.40.0.tar.gz && rm -rf mBPCR.buildbin-libdir && mkdir mBPCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mBPCR.buildbin-libdir mBPCR_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL mBPCR_1.40.0.zip && rm mBPCR_1.40.0.tar.gz mBPCR_1.40.0.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 450k 100 450k 0 0 6600k 0 --:--:-- --:--:-- --:--:-- 7044k
install for i386
* installing *source* package 'mBPCR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'SNPchip' is deprecated and will be removed from Bioconductor
version 3.11
** help
*** installing help indices
converting help for package 'mBPCR'
finding HTML links ... done
computeMBPCR html
estGlobParam html
estProfileWithMBPCR html
estProfileWithMBPCRforOligoSnpSet html
importCNData html
jekoChr11Array250Knsp html
logAdd html
mBPCR-internal html
plotEstProfile html
rec10k html
writeEstProfile html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'SNPchip' is deprecated and will be removed from Bioconductor
version 3.11
** testing if installed package can be loaded from final location
Warning: Package 'SNPchip' is deprecated and will be removed from Bioconductor
version 3.11
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'mBPCR' ...
** testing if installed package can be loaded
Warning: Package 'SNPchip' is deprecated and will be removed from Bioconductor
version 3.11
* MD5 sums
packaged installation of 'mBPCR' as mBPCR_1.40.0.zip
* DONE (mBPCR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'mBPCR' successfully unpacked and MD5 sums checked
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mBPCR.Rcheck/examples_i386/mBPCR-Ex.timings
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mBPCR.Rcheck/examples_x64/mBPCR-Ex.timings
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