inveRsion 1.24.1
Alejandro Caceres
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/inveRsion | | Last Changed Rev: 129423 / Revision: 131943 | | Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings inveRsion_1.24.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/inveRsion.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘inveRsion/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘inveRsion’ version ‘1.24.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘inveRsion’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’
A package should be listed in only one of these fields.
* 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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘haplo.stats’
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
File ‘inveRsion/R/zzz.R’:
.onLoad calls:
packageStartupMessage("\n")
packageStartupMessage("Hola!\n")
packageStartupMessage("welcome to inevRsion package. \n \n \n")
packageStartupMessage("type: manual() for full manual \n vignette(\"inveRsion\") for a quick start \n")
See section ‘Good practice’ in '?.onAttach'.
callEncode: no visible global function definition for ‘quantile’
encodeGeno: no visible global function definition for ‘setupGeno’
encodeGeno: no visible global function definition for ‘haplo.em’
encodeGeno: no visible global function definition for
‘haplo.em.control’
encodeGenoAcross: no visible global function definition for ‘setupGeno’
encodeGenoAcross: no visible global function definition for ‘haplo.em’
encodeGenoAcross: no visible global function definition for
‘haplo.em.control’
Undefined global functions or variables:
haplo.em haplo.em.control quantile setupGeno
Consider adding
importFrom("stats", "quantile")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/inveRsion.Rcheck/00check.log’
for details.
* installing *source* package ‘inveRsion’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init_inveRsion.c -o init_inveRsion.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c inversionModel.c -o inversionModel.o
inversionModel.c: In function ‘blockAndLev’:
inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if(dat[(*nr)*(c1)+row]==levelleft[level] & dat[(*nr)*(c2)+row]==levelright[level])
^
inversionModel.c: In function ‘inversionModel’:
inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
while(steps<*maxSteps & tol>mintol)
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c writeGenoDat.c -o writeGenoDat.o
writeGenoDat.c: In function ‘writeGenoDat’:
writeGenoDat.c:85:6: warning: ‘dat’ may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(dat){
^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o inveRsion.so init_inveRsion.o inversionModel.o writeGenoDat.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/inveRsion.Rcheck/inveRsion/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (inveRsion)