Samsiddhi Bhattacharjee
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ASSET |
| Branch: RELEASE_3_9 |
| Last Commit: a32763e |
| Last Changed Date: 2019-05-02 11:53:44 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:28:25 -0400 (Wed, 16 Oct 2019).
| Package 89/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ASSET 2.2.0 Samsiddhi Bhattacharjee
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ASSET |
| Version: 2.2.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASSET.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ASSET_2.2.0.tar.gz |
| StartedAt: 2019-10-16 02:00:46 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:02:28 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 102.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ASSET.Rcheck |
| Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASSET.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ASSET_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ASSET.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ASSET/DESCRIPTION' ... OK * this is package 'ASSET' version '2.2.0' * 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 'ASSET' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpmEXFGe/R.INSTALL8dc78be5b61/ASSET/man/h.traits.Rd:41: missing link 'p.tube' Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpmEXFGe/R.INSTALL8dc78be5b61/ASSET/man/h.types.Rd:38: missing link 'p.tube' See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ASSET.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. License components with restrictions not permitted: GPL-2 + file LICENSE * 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 Package in Depends field not imported from: 'rmeta' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE dlm.pval: no visible global function definition for 'pnorm' getCI: no visible global function definition for 'qnorm' h.forest: no visible global function definition for 'meta.colors' h.forest: no visible global function definition for 'title' h.traits1: no visible global function definition for 'qnorm' h.traits2: no visible global function definition for 'pchisq' h.types0: no visible global function definition for 'qnorm' p.bon: no visible global function definition for 'pnorm' qxd.prod.coef: no visible global function definition for 'pnorm' qxd.prod.cor: no visible global function definition for 'pnorm' qxd.prod.int: no visible global function definition for 'integrate' qxd.prod.int :: no visible global function definition for 'dnorm' traits.forest: no visible global function definition for 'pnorm' traits.forest0: no visible global function definition for 'pnorm' traits.meta: no visible global function definition for 'pnorm' tube.pval: no visible global function definition for 'pnorm' tubeSim: no visible global function definition for 'rnorm' types.score: no visible global function definition for 'model.matrix' types.score: no visible global function definition for 'as.formula' types.score: no visible global function definition for 'glm' types.score: no visible global function definition for 'binomial' types.wald: no visible global function definition for 'model.frame' types.wald: no visible global function definition for 'as.formula' types.wald : : no visible global function definition for 'glm' types.wald : : no visible global function definition for 'binomial' types.wald : : no visible global function definition for 'as.formula' types.wald: no visible global function definition for 'pnorm' z.max: no visible global function definition for 'pnorm' Undefined global functions or variables: as.formula binomial dnorm glm integrate meta.colors model.frame model.matrix pchisq pnorm qnorm rnorm title Consider adding importFrom("graphics", "title") importFrom("stats", "as.formula", "binomial", "dnorm", "glm", "integrate", "model.frame", "model.matrix", "pchisq", "pnorm", "qnorm", "rnorm") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'h.traits.Rd': 'p.tube' Missing link or links in documentation object 'h.types.Rd': 'p.tube' See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: 'p.tube' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 h.types 6.85 0.15 7 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed h.types 8.15 0.1 8.25 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.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: 3 WARNINGs, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ASSET.Rcheck/00check.log' for details.
ASSET.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ASSET_2.2.0.tar.gz && rm -rf ASSET.buildbin-libdir && mkdir ASSET.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASSET.buildbin-libdir ASSET_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ASSET_2.2.0.zip && rm ASSET_2.2.0.tar.gz ASSET_2.2.0.zip
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install for i386
* installing *source* package 'ASSET' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ASSET'
finding HTML links ... done
ASSET html
ex_trait html
ex_types html
h.forestPlot html
h.summary html
h.traits html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpmEXFGe/R.INSTALL8dc78be5b61/ASSET/man/h.traits.Rd:41: missing link 'p.tube'
h.types html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpmEXFGe/R.INSTALL8dc78be5b61/ASSET/man/h.types.Rd:38: missing link 'p.tube'
p.dlm html
z.max 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 'ASSET' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASSET' as ASSET_2.2.0.zip
* DONE (ASSET)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ASSET' successfully unpacked and MD5 sums checked
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ASSET.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("ASSET")
RUNIT TEST PROTOCOL -- Wed Oct 16 02:02:16 2019
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
ASSET RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
7.57 0.26 7.95
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ASSET.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("ASSET")
RUNIT TEST PROTOCOL -- Wed Oct 16 02:02:23 2019
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
ASSET RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
7.21 0.12 7.32
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ASSET.Rcheck/examples_i386/ASSET-Ex.timings
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ASSET.Rcheck/examples_x64/ASSET-Ex.timings
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