Marzia A Cremona
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/IWTomics |
| Branch: RELEASE_3_11 |
| Last Commit: 8af16ce |
| Last Changed Date: 2020-04-27 15:03:49 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:55 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE IWTomics PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 912/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IWTomics 1.12.0 Marzia A Cremona
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: IWTomics |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IWTomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings IWTomics_1.12.0.tar.gz |
| StartedAt: 2020-10-17 05:25:32 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:31:59 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 386.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: IWTomics.Rcheck |
| Warnings: 2 |
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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:IWTomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings IWTomics_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/IWTomics.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 'IWTomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IWTomics' version '1.12.0'
* 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 'IWTomics' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:60: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:135: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:168: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:308: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:309: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsTest.Rd:61: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsTest.Rd:64: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsTest.Rd:79: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsTest.Rd:80: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/plot-IWTomicsData.Rd:96: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/regions_example.Rd:19: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/regions_example.Rd:15: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/smooth-IWTomicsData.Rd:78: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/IWTomics.Rcheck/00install.out' for details.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
plot.IWTomicsData
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... WARNING
Warning: package needs dependence on R (>= 2.10)
* 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
IWTomicsTest 68.06 0.25 68.34
IWTomicsData-class 12.33 0.02 12.36
IWTomics-package 9.91 1.57 11.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
IWTomicsTest 70.70 0.89 71.66
IWTomicsData-class 12.72 0.02 12.73
IWTomics-package 9.78 1.61 11.40
plotSummary 6.28 0.07 6.38
* 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 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/IWTomics.Rcheck/00check.log'
for details.
IWTomics.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/IWTomics_1.12.0.tar.gz && rm -rf IWTomics.buildbin-libdir && mkdir IWTomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IWTomics.buildbin-libdir IWTomics_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL IWTomics_1.12.0.zip && rm IWTomics_1.12.0.tar.gz IWTomics_1.12.0.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 682k 100 682k 0 0 6399k 0 --:--:-- --:--:-- --:--:-- 6752k
install for i386
* installing *source* package 'IWTomics' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'smooth' in package 'IWTomics'
** help
*** installing help indices
converting help for package 'IWTomics'
finding HTML links ... done
ETn_example html
IWTomics-internal html
IWTomics-package html
IWTomicsData-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:60: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:135: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:168: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:308: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsData-class.Rd:309: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
IWTomicsTest html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsTest.Rd:61: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsTest.Rd:64: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsTest.Rd:79: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/IWTomicsTest.Rd:80: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
features_example html
plot-IWTomicsData html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/plot-IWTomicsData.Rd:96: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
plotSummary html
plotTest html
regionsFeatures_center html
regionsFeatures_scale html
regions_example html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/regions_example.Rd:19: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/regions_example.Rd:15: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
smooth-IWTomicsData html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMhkbmY/R.INSTALL1c7831d30c9/IWTomics/man/smooth-IWTomicsData.Rd:78: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
** 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 'IWTomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IWTomics' as IWTomics_1.12.0.zip
* DONE (IWTomics)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'IWTomics' successfully unpacked and MD5 sums checked
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IWTomics.Rcheck/examples_i386/IWTomics-Ex.timings
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IWTomics.Rcheck/examples_x64/IWTomics-Ex.timings
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