mgsa 1.24.0
Sebastian Bauer
| 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/mgsa | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf mgsa.buildbin-libdir mgsa.Rcheck && mkdir mgsa.buildbin-libdir mgsa.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mgsa.buildbin-libdir mgsa_1.24.0.tar.gz >mgsa.Rcheck\00install.out 2>&1 && cp mgsa.Rcheck\00install.out mgsa-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=mgsa.buildbin-libdir --install="check:mgsa-install.out" --force-multiarch --no-vignettes --timings mgsa_1.24.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/mgsa.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mgsa/DESCRIPTION' ... OK
* this is package 'mgsa' version '1.24.0'
* 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 'mgsa' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... 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
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'mgsa' for: 'show'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... 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 ... NOTE
Warning: no function found corresponding to methods exports from 'mgsa' for: 'show'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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
'library' or 'require' call to 'gplots' which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
'DBI' 'GO.db' 'RSQLite'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
'stats' 'utils'
All declared Imports should be used.
Packages in Depends field not imported from:
'gplots' 'methods'
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
createMgsaGoSets: no visible global function definition for 'new'
mcmcSummary: no visible binding for global variable 'sd'
mgsa.wrapper: no visible global function definition for 'str'
mgsa.wrapper: no visible global function definition for 'new'
readGAF: no visible global function definition for 'read.delim'
readGAF: no visible global function definition for 'na.omit'
readGAF: no visible global function definition for 'new'
initialize,MgsaSets: no visible global function definition for
'callNextMethod'
initialize,MgsaSets: no visible global function definition for 'relist'
mgsa,character-MgsaSets: no visible global function definition for
'na.omit'
plot,MgsaResults: no visible global function definition for
'split.screen'
plot,MgsaResults: no visible global function definition for 'screen'
plot,MgsaResults: no visible global function definition for 'par'
plot,MgsaResults: no visible global function definition for 'barplot2'
plot,MgsaResults: no visible global function definition for
'close.screen'
Undefined global functions or variables:
barplot2 callNextMethod close.screen na.omit new par read.delim
relist screen sd split.screen str
Consider adding
importFrom("graphics", "close.screen", "par", "screen", "split.screen")
importFrom("methods", "callNextMethod", "new")
importFrom("stats", "na.omit", "sd")
importFrom("utils", "read.delim", "relist", "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 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 ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/mgsa.buildbin-libdir/mgsa/libs/i386/mgsa.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
readGAF 4.4 0.61 5.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
readGAF 5.92 0.75 6.68
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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: 1 WARNING, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/mgsa.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'mgsa' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mgsa-core.c -o mgsa-core.o
mgsa-core.c: In function 'ts_R_alloc':
mgsa-core.c:56:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
^
mgsa-core.c: At top level:
mgsa-core.c:796:13: warning: 'print_context' defined but not used [-Wunused-function]
static void print_context(struct context *cn)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mgsa.c -o mgsa.o
mgsa.c: In function 'create_parameter_prior_from_R':
mgsa.c:52:10: warning: assignment from incompatible pointer type
if (!(p = R_alloc(1,sizeof(*p))))
^
mgsa.c:65:19: warning: assignment from incompatible pointer type
if (!(p->values = R_alloc(p->number_of_states,sizeof(p->values[0]))))
^
mgsa.c: In function 'create_summary_for_param_from_R':
mgsa.c:177:19: warning: assignment from incompatible pointer type
if (!(sum->dmap = R_alloc(number_of_discrete_values,sizeof(sum->dmap[0]))))
^
mgsa.c: In function 'mgsa_mcmc':
mgsa.c:407:7: warning: assignment from incompatible pointer type
nas = R_alloc(las,sizeof(nas[0]));
^
mgsa.c:548:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
mgsa.c:554:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mt.c -o mt.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o mgsa.dll tmp.def mgsa-core.o mgsa.o mt.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/mgsa.buildbin-libdir/mgsa/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'mgsa' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mgsa-core.c -o mgsa-core.o
mgsa-core.c: In function 'ts_R_alloc':
mgsa-core.c:56:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
^
mgsa-core.c: At top level:
mgsa-core.c:796:13: warning: 'print_context' defined but not used [-Wunused-function]
static void print_context(struct context *cn)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mgsa.c -o mgsa.o
mgsa.c: In function 'create_parameter_prior_from_R':
mgsa.c:52:10: warning: assignment from incompatible pointer type
if (!(p = R_alloc(1,sizeof(*p))))
^
mgsa.c:65:19: warning: assignment from incompatible pointer type
if (!(p->values = R_alloc(p->number_of_states,sizeof(p->values[0]))))
^
mgsa.c: In function 'create_summary_for_param_from_R':
mgsa.c:177:19: warning: assignment from incompatible pointer type
if (!(sum->dmap = R_alloc(number_of_discrete_values,sizeof(sum->dmap[0]))))
^
mgsa.c: In function 'mgsa_mcmc':
mgsa.c:407:7: warning: assignment from incompatible pointer type
nas = R_alloc(las,sizeof(nas[0]));
^
mgsa.c:548:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
mgsa.c:554:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mt.c -o mt.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o mgsa.dll tmp.def mgsa-core.o mgsa.o mt.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/mgsa.buildbin-libdir/mgsa/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mgsa' as mgsa_1.24.0.zip
* DONE (mgsa)