brian-j-smith/magma — pull request #1 by sgsokol (2014-10-07 16:43:23+00:00)
Title: v 1.5.0-1

Hi Brian,

Getting familiar with github took some time but here is my proposal for commit.
While cheking by automatic R tool I've got the following output:
[root@gba-03264 R]# R CMD check --as-cran --install-args="--configure-args='--with-lapack=/usr/local/atlas/lib64/libsatlas.so --with-magma-home=/usr/local/src/magma-1.5.0 --with-r-home=/usr/local/src/R-3.1.1'" magma_1.5.0-1.tar.gz
* using log directory ‘/home/sokol/dev/R/magma.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘magma/DESCRIPTION’ ... OK
* this is package ‘magma’ version ‘1.5.0-1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Brian J. Smith ’
New maintainer:
Brian J. Smith
Old maintainer(s):
Brian J Smith
CRAN repository db overrides:
OS_type: unix
* checking package namespace information ... OK
* checking package dependencies ... NOTE
No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘magma’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
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
* 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
le package 'methods' est utilisé mais pas déclaré
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* 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 line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/sokol/dev/R/magma.Rcheck/magma/libs/magma.so’:
Found ‘exit’, possibly from ‘exit’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
!pdfTeX error: pdflatex (file ec-inconsolata): Font ec-inconsolata at 540 not f
ound
==> Fatal error occurred, no output PDF file produced!
* checking PDF version of manual without hyperrefs or index ... OK

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
‘/home/sokol/dev/R/magma.Rcheck/00check.log’
for details.

Please review and commit if everything is OK.

Best,
Serguei.