R Development Page

bigPSD log file (check_x86_64_linux)

Thu Nov 12 10:44:09 2015: Checking package bigPSD (SVN revision 43) ...
* using log directory ‘/mnt/building/build_2015-11-12-10-14/RF_PKG_CHECK/PKGS/bigPSD.Rcheck’
* using R version 3.2.2 Patched (2015-11-06 r69607)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘bigPSD/DESCRIPTION’ ... OK
* this is package ‘bigPSD’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Paulino Perez ’
New submission
Found the following (possibly) invalid URLs:
  URL: http://www.aspect-sdm.org/Parallel-R
    From: man/Rquit.Rd
    Status: 404
    Message: Not Found

No package encoding and non-ASCII characters in the following R files:
  R/HLRscalapack.R
    2: #   R-ScaLAPACK version 0.4.x: ScaLAPACK interface to R
    3: #    Oak Ridge National Laboratory, Oak Ridge TN.
    4: #       Authors: David Bauer, Guruprasad Kora, Nagiza. F. Samatova, 
    6: #Contact: Nagiza F. Samatova; (865) 241-4351; samatovan@ornl.gov
    8: #Computer Science and Mathematics Division
    9: #Oak Ridge National Laboratory, Oak Ridge TN 37831 
    10: # (C) 2004 All Rights Reserved
    12: # NOTICE
    22: # purpose. This software is provided ``as is'' without express or
  R/ParallelAgent.R
    2: #   R-ScaLAPACK version 0.4.x: ScaLAPACK interface to R
    3: #    Oak Ridge National Laboratory, Oak Ridge TN.
    4: #       Authors: David Bauer, Guruprasad Kora, Nagiza. F. Samatova, 
    6: #Contact: Nagiza F. Samatova; (865) 241-4351; samatovan@ornl.gov
    8: #Computer Science and Mathematics Division
    9: #Oak Ridge National Laboratory, Oak Ridge TN 37831 
    10: # (C) 2004 All Rights Reserved
    12: # NOTICE
    22: # purpose. This software is provided ``as is'' without express or
  R/Rscalapack.R
    2: #   R-bigPSD version 0.4.x: bigPSD interface to R
    3: #    Oak Ridge National Laboratory, Oak Ridge TN.
    4: #       Authors: David Bauer, Guruprasad Kora, Nagiza. F. Samatova, 
    6: #Contact: Nagiza F. Samatova; (865) 241-4351; samatovan@ornl.gov
    8: #Computer Science and Mathematics Division
    9: #Oak Ridge National Laboratory, Oak Ridge TN 37831 
    10: # (C) 2004 All Rights Reserved
    12: # NOTICE
    22: # purpose. This software is provided ``as is'' without express or

The Title field should be in title case, current version then in title case:
‘Computation of genomic relationship matrixes and genomic distances. This version uses a subset of functions originally found in the package RScaLAPACK (0.6.1).’
‘Computation of Genomic Relationship Matrixes and Genomic Distances. This Version Uses a Subset of Functions Originally Found in the Package RScaLAPACK (0.6.1).’

The Date field is over a month old.
* 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 ‘bigPSD’ can be installed ... [94s/104s] WARNING
Found the following significant warnings:
  CRDriver.c:40:9: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/mnt/building/build_2015-11-12-10-14/RF_PKG_CHECK/PKGS/bigPSD.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘history.txt’
* checking for left-over files ... OK
* checking index information ... WARNING
Demos with missing or empty index information:
[1] "read_sub_matrix"
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
* checking package subdirectories ... WARNING
Demos with non-ASCII characters:  RScaLAPACK.R
Portable packages must use only ASCII characters in their demos.
Use \uxxxx escapes for other characters.
* 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 use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
sla.ProcessRowsColumns: no visible binding for global variable
  ‘.RscalaGrid’

Found the following assignments to the global environment:
File ‘bigPSD/R/Rscalapack.R’:
  assign(".RscalaGrid", .RscalaGrid, envir = .GlobalEnv)
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'Rprincomp.Rd':
  \usage lines wider than 90 characters:
     sla.princomp(x, cor = FALSE, scores = TRUE, covmat = NULL, subset = rep(TRUE, nrow(as.matrix(x))), NPROWS=0, NPCOLS=0, MB=16, ...)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘G_matrix’ ‘readBinLT1’ ‘readLT1’ ‘read_sub_matrix’ ‘sla.tcrossprod’
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
  apparently PKG_LIBS is missing $(FLIBS) in ‘src/Makefile’
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/mnt/building/build_2015-11-12-10-14/RF_PKG_CHECK/PKGS/bigPSD.Rcheck/bigPSD/libs/bigPSD.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 ... [0s/0s] OK
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 7 NOTEs
See
  ‘/mnt/building/build_2015-11-12-10-14/RF_PKG_CHECK/PKGS/bigPSD.Rcheck/00check.log’
for details.


Run time: 150.76 seconds.