Michal Okoniewski
| Snapshot Date: 2018-10-28 16:46:29 -0400 (Sun, 28 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ampliQueso |
| Branch: master |
| Last Commit: 1e2c703 |
| Last Changed Date: 2018-10-18 08:06:35 -0400 (Thu, 18 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2018-10-29 10:26:47 -0400 (Mon, 29 Oct 2018).
| Package 45/1642 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Michal Okoniewski
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ampliQueso |
| Version: 1.19.4 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ampliQueso.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ampliQueso_1.19.4.tar.gz |
| StartedAt: 2018-10-29 01:28:13 -0400 (Mon, 29 Oct 2018) |
| EndedAt: 2018-10-29 01:35:21 -0400 (Mon, 29 Oct 2018) |
| EllapsedTime: 428.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ampliQueso.Rcheck |
| Warnings: 4 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ampliQueso.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ampliQueso_1.19.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ampliQueso.Rcheck'
* using R Under development (unstable) (2018-10-22 r75479)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ampliQueso/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ampliQueso' version '1.19.4'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'rnaSeqMap', 'knitr', 'rgl', 'ggplot2', 'gplots', 'parallel',
'doParallel', 'foreach', 'VariantAnnotation', 'genefilter',
'statmod', 'xtable'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'ampliQueso' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'ampliQueso' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ampliQueso.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 ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: 'BiocManager'
Namespace in Imports field not imported from: 'samr'
All declared Imports should be used.
Packages in Depends field not imported from:
'VariantAnnotation' 'doParallel' 'foreach' 'genefilter' 'ggplot2'
'gplots' 'knitr' 'parallel' 'rgl' 'statmod' 'xtable'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': 'rnaSeqMap:::newSeqReads'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.callCamelTestReg: no visible global function definition for 'permp'
.callSamPileup: no visible global function definition for 'hasArg'
.callSamPileup: no visible global function definition for 'readVcf'
.callSamPileup: no visible global function definition for 'seqnames'
.callSamPileup: no visible global function definition for 'start'
.callSamPileup: no visible global function definition for 'ranges'
.callSamPileup: no visible global function definition for 'end'
.callSamPileup: no visible global function definition for 'width'
.callSamPileup: no visible global function definition for 'ref'
.callSamPileup: no visible global function definition for 'strand'
.callSamPileup: no visible global function definition for 'qual'
.camelTest: no visible global function definition for 'read.table'
.camelTest: no visible binding for global variable 'str'
.camelTest: no visible global function definition for 'permp'
.camelTestParReg: no visible global function definition for
'read.table'
.camelTestParReg: no visible global function definition for
'makeCluster'
.camelTestParReg: no visible global function definition for
'detectCores'
.camelTestParReg: no visible global function definition for
'registerDoParallel'
.camelTestParReg: no visible global function definition for '%dopar%'
.camelTestParReg: no visible global function definition for 'foreach'
.camelTestParReg: no visible global function definition for
'stopCluster'
.compareCoveragesRegApply: no visible global function definition for
'read.table'
.compareCoveragesRegParM: no visible global function definition for
'read.table'
.compareCoveragesRegParM: no visible global function definition for
'makeCluster'
.compareCoveragesRegParM: no visible global function definition for
'detectCores'
.compareCoveragesRegParM: no visible global function definition for
'registerDoParallel'
.compareCoveragesRegParM: no visible global function definition for
'%dopar%'
.compareCoveragesRegParM: no visible global function definition for
'foreach'
.compareCoveragesRegParM: no visible global function definition for
'stopCluster'
.compareCoveragesRegParR: no visible global function definition for
'read.table'
.compareCoveragesRegParR: no visible global function definition for
'makeCluster'
.compareCoveragesRegParR: no visible global function definition for
'detectCores'
.compareCoveragesRegParR: no visible global function definition for
'registerDoParallel'
.compareCoveragesRegParR: no visible global function definition for
'%dopar%'
.compareCoveragesRegParR: no visible global function definition for
'foreach'
.compareCoveragesRegParR: no visible global function definition for
'stopCluster'
.compareCoveragesRegSeq: no visible global function definition for
'read.table'
.getSNP: no visible global function definition for 'read.table'
.getSNP: no visible global function definition for 'hasArg'
.getSNP: no visible global function definition for 'readVcf'
.getSNP: no visible global function definition for 'seqnames'
.getSNP: no visible global function definition for 'start'
.getSNP: no visible global function definition for 'ranges'
.getSNP: no visible global function definition for 'end'
.getSNP: no visible global function definition for 'width'
.getSNP: no visible global function definition for 'ref'
.getSNP: no visible global function definition for 'strand'
.getSNP: no visible global function definition for 'qual'
.getSNPPar: no visible global function definition for 'makeCluster'
.getSNPPar: no visible global function definition for 'detectCores'
.getSNPPar: no visible global function definition for
'registerDoParallel'
.getSNPPar: no visible global function definition for 'read.table'
.getSNPPar: no visible global function definition for '%dopar%'
.getSNPPar: no visible global function definition for 'foreach'
.getSNPPar: no visible global function definition for 'stopCluster'
.loadLibs: no visible global function definition for 'install.packages'
.perm.samples: no visible global function definition for 'combn'
compareCoverages: no visible global function definition for
'read.table'
getCountTable: no visible global function definition for 'read.table'
runAQReport: no visible global function definition for 'read.table'
runAQReport: no visible global function definition for 'rowttests'
runAQReport: no visible global function definition for 'p.adjust'
runAQReport: no visible global function definition for '%do%'
runAQReport: no visible global function definition for 'foreach'
runAQReport: no visible global function definition for 'aggregate'
runAQReport: no visible global function definition for 'knit'
Undefined global functions or variables:
%do% %dopar% aggregate combn detectCores end foreach hasArg
install.packages knit makeCluster p.adjust permp qual ranges
read.table readVcf ref registerDoParallel rowttests seqnames start
stopCluster str strand width
Consider adding
importFrom("methods", "hasArg")
importFrom("stats", "aggregate", "end", "p.adjust", "start")
importFrom("utils", "combn", "install.packages", "read.table", "str")
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' ... WARNING
Found the following significant warnings:
Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/ampliQueso', resetting
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/ampliQueso', resetting
* 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: 4 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/ampliQueso.Rcheck/00check.log'
for details.
ampliQueso.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ampliQueso_1.19.4.tar.gz && rm -rf ampliQueso.buildbin-libdir && mkdir ampliQueso.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ampliQueso.buildbin-libdir ampliQueso_1.19.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ampliQueso_1.19.4.zip && rm ampliQueso_1.19.4.tar.gz ampliQueso_1.19.4.zip
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install for i386
* installing *source* package 'ampliQueso' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ampliQueso'
finding HTML links ... done
camelSampleTable html
camelTest html
compareCoverages html
compareCoveragesReg html
getCountTable html
getSNP html
ndMax html
ndMin html
runAQReport html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'ampliQueso' is deprecated and will be removed from
Bioconductor version 3.9
In R CMD INSTALL
install for x64
* installing *source* package 'ampliQueso' ...
** testing if installed package can be loaded
Warning: Package 'ampliQueso' is deprecated and will be removed from
Bioconductor version 3.9
* MD5 sums
packaged installation of 'ampliQueso' as ampliQueso_1.19.4.zip
* DONE (ampliQueso)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ampliQueso' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
ampliQueso.Rcheck/examples_i386/ampliQueso-Ex.timings
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ampliQueso.Rcheck/examples_x64/ampliQueso-Ex.timings
|