eiR 1.11.0
Thomas Girke
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/eiR | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings eiR_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/eiR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eiR’ version ‘1.11.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘eiR’ can be installed ... [33s/33s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘ChemmineR’ ‘RCurl’ ‘snow’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
Namespaces in Imports field not imported from:
‘BiocGenerics’ ‘RCurl’ ‘RUnit’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
insertEmbeddedDescriptors: no visible global function definition for
‘dbGetPreparedQuery’
insertEmbeddedDescriptors: no visible global function definition for
‘postgresqlWriteTable’
insertEmbeddedDescriptorsByCompoundId: no visible global function
definition for ‘dbGetPreparedQuery’
insertEmbeddedDescriptorsByCompoundId: no visible global function
definition for ‘postgresqlWriteTable’
insertGroupMembers: no visible global function definition for
‘dbGetPreparedQuery’
insertGroupMembers: no visible global function definition for
‘postgresqlWriteTable’
Undefined global functions or variables:
dbGetPreparedQuery postgresqlWriteTable
* 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
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
File ‘eiR/libs/eiR.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Objects: ‘apost.o’, ‘format.o’, ‘recordfile.o’, ‘scan.o’
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Objects: ‘apost.o’, ‘format.o’, ‘profiling.o’
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.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
eiPerformanceTest 7.214 0.260 7.489
eiCluster 5.027 0.249 5.277
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [27s/37s]
[28s/38s] 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, 7 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/eiR.Rcheck/00check.log’
for details.
* installing *source* package ‘eiR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c apost.cpp -o apost.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c char_bit_cnt.cpp -o char_bit_cnt.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c embedCoords.cc -o embedCoords.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c eucsearch.cc -o eucsearch.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c format.cc -o format.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c mplsh-model.cpp -o mplsh-model.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c mplsh.cpp -o mplsh.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c profiling.cc -o profiling.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c r_wrap.cpp -o r_wrap.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c recordfile.cc -o recordfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c routines.c -o routines.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c scan.cc -o scan.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c search_r.cpp -o search_r.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -c solver.cc -o solver.o
make[1]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/eiR.Rcheck/00_pkg_src/eiR/src/f2c'
cp signal1.h0 signal1.h
cp sysdep1.h0 sysdep1.h
gcc -std=gnu99 -c f77vers.c
gcc -std=gnu99 -c i77vers.c
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic main.c
ld -r -x -o main.xxx main.o
mv main.xxx main.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic s_rnge.c
ld -r -x -o s_rnge.xxx s_rnge.o
mv s_rnge.xxx s_rnge.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic abort_.c
ld -r -x -o abort_.xxx abort_.o
mv abort_.xxx abort_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic exit_.c
ld -r -x -o exit_.xxx exit_.o
mv exit_.xxx exit_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic getarg_.c
ld -r -x -o getarg_.xxx getarg_.o
mv getarg_.xxx getarg_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic iargc_.c
ld -r -x -o iargc_.xxx iargc_.o
mv iargc_.xxx iargc_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic getenv_.c
ld -r -x -o getenv_.xxx getenv_.o
mv getenv_.xxx getenv_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic signal_.c
ld -r -x -o signal_.xxx signal_.o
mv signal_.xxx signal_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic s_stop.c
ld -r -x -o s_stop.xxx s_stop.o
mv s_stop.xxx s_stop.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic s_paus.c
ld -r -x -o s_paus.xxx s_paus.o
mv s_paus.xxx s_paus.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic system_.c
ld -r -x -o system_.xxx system_.o
mv system_.xxx system_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic cabs.c
ld -r -x -o cabs.xxx cabs.o
mv cabs.xxx cabs.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic ctype.c
ld -r -x -o ctype.xxx ctype.o
mv ctype.xxx ctype.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic derf_.c
ld -r -x -o derf_.xxx derf_.o
mv derf_.xxx derf_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic derfc_.c
ld -r -x -o derfc_.xxx derfc_.o
mv derfc_.xxx derfc_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic erf_.c
ld -r -x -o erf_.xxx erf_.o
mv erf_.xxx erf_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic erfc_.c
ld -r -x -o erfc_.xxx erfc_.o
mv erfc_.xxx erfc_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic sig_die.c
ld -r -x -o sig_die.xxx sig_die.o
mv sig_die.xxx sig_die.o
gcc -std=gnu99 -o a.out -g -O2 -fpic -DNO_FPINIT arithchk.c -lm ||\
gcc -std=gnu99 -o a.out -DNO_LONG_LONG -g -O2 -fpic -DNO_FPINIT arithchk.c -lm
./a.out >arith.h
rm -f a.out arithchk.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic uninit.c
ld -r -x -o uninit.xxx uninit.o
mv uninit.xxx uninit.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic pow_ci.c
ld -r -x -o pow_ci.xxx pow_ci.o
mv pow_ci.xxx pow_ci.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic pow_dd.c
ld -r -x -o pow_dd.xxx pow_dd.o
mv pow_dd.xxx pow_dd.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic pow_di.c
ld -r -x -o pow_di.xxx pow_di.o
mv pow_di.xxx pow_di.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic pow_hh.c
ld -r -x -o pow_hh.xxx pow_hh.o
mv pow_hh.xxx pow_hh.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic pow_ii.c
ld -r -x -o pow_ii.xxx pow_ii.o
mv pow_ii.xxx pow_ii.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic pow_ri.c
ld -r -x -o pow_ri.xxx pow_ri.o
mv pow_ri.xxx pow_ri.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic pow_zi.c
ld -r -x -o pow_zi.xxx pow_zi.o
mv pow_zi.xxx pow_zi.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic pow_zz.c
ld -r -x -o pow_zz.xxx pow_zz.o
mv pow_zz.xxx pow_zz.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic c_abs.c
ld -r -x -o c_abs.xxx c_abs.o
mv c_abs.xxx c_abs.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic c_cos.c
ld -r -x -o c_cos.xxx c_cos.o
mv c_cos.xxx c_cos.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic c_div.c
ld -r -x -o c_div.xxx c_div.o
mv c_div.xxx c_div.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic c_exp.c
ld -r -x -o c_exp.xxx c_exp.o
mv c_exp.xxx c_exp.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic c_log.c
ld -r -x -o c_log.xxx c_log.o
mv c_log.xxx c_log.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic c_sin.c
ld -r -x -o c_sin.xxx c_sin.o
mv c_sin.xxx c_sin.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic c_sqrt.c
ld -r -x -o c_sqrt.xxx c_sqrt.o
mv c_sqrt.xxx c_sqrt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic z_abs.c
ld -r -x -o z_abs.xxx z_abs.o
mv z_abs.xxx z_abs.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic z_cos.c
ld -r -x -o z_cos.xxx z_cos.o
mv z_cos.xxx z_cos.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic z_div.c
ld -r -x -o z_div.xxx z_div.o
mv z_div.xxx z_div.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic z_exp.c
ld -r -x -o z_exp.xxx z_exp.o
mv z_exp.xxx z_exp.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic z_log.c
ld -r -x -o z_log.xxx z_log.o
mv z_log.xxx z_log.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic z_sin.c
ld -r -x -o z_sin.xxx z_sin.o
mv z_sin.xxx z_sin.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic z_sqrt.c
ld -r -x -o z_sqrt.xxx z_sqrt.o
mv z_sqrt.xxx z_sqrt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_abs.c
ld -r -x -o r_abs.xxx r_abs.o
mv r_abs.xxx r_abs.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_acos.c
ld -r -x -o r_acos.xxx r_acos.o
mv r_acos.xxx r_acos.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_asin.c
ld -r -x -o r_asin.xxx r_asin.o
mv r_asin.xxx r_asin.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_atan.c
ld -r -x -o r_atan.xxx r_atan.o
mv r_atan.xxx r_atan.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_atn2.c
ld -r -x -o r_atn2.xxx r_atn2.o
mv r_atn2.xxx r_atn2.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_cnjg.c
ld -r -x -o r_cnjg.xxx r_cnjg.o
mv r_cnjg.xxx r_cnjg.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_cos.c
ld -r -x -o r_cos.xxx r_cos.o
mv r_cos.xxx r_cos.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_cosh.c
ld -r -x -o r_cosh.xxx r_cosh.o
mv r_cosh.xxx r_cosh.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_dim.c
ld -r -x -o r_dim.xxx r_dim.o
mv r_dim.xxx r_dim.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_exp.c
ld -r -x -o r_exp.xxx r_exp.o
mv r_exp.xxx r_exp.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_imag.c
ld -r -x -o r_imag.xxx r_imag.o
mv r_imag.xxx r_imag.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_int.c
ld -r -x -o r_int.xxx r_int.o
mv r_int.xxx r_int.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_lg10.c
ld -r -x -o r_lg10.xxx r_lg10.o
mv r_lg10.xxx r_lg10.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_log.c
ld -r -x -o r_log.xxx r_log.o
mv r_log.xxx r_log.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_mod.c
ld -r -x -o r_mod.xxx r_mod.o
mv r_mod.xxx r_mod.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_nint.c
ld -r -x -o r_nint.xxx r_nint.o
mv r_nint.xxx r_nint.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_sign.c
ld -r -x -o r_sign.xxx r_sign.o
mv r_sign.xxx r_sign.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_sin.c
ld -r -x -o r_sin.xxx r_sin.o
mv r_sin.xxx r_sin.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_sinh.c
ld -r -x -o r_sinh.xxx r_sinh.o
mv r_sinh.xxx r_sinh.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_sqrt.c
ld -r -x -o r_sqrt.xxx r_sqrt.o
mv r_sqrt.xxx r_sqrt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_tan.c
ld -r -x -o r_tan.xxx r_tan.o
mv r_tan.xxx r_tan.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic r_tanh.c
ld -r -x -o r_tanh.xxx r_tanh.o
mv r_tanh.xxx r_tanh.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_abs.c
ld -r -x -o d_abs.xxx d_abs.o
mv d_abs.xxx d_abs.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_acos.c
ld -r -x -o d_acos.xxx d_acos.o
mv d_acos.xxx d_acos.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_asin.c
ld -r -x -o d_asin.xxx d_asin.o
mv d_asin.xxx d_asin.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_atan.c
ld -r -x -o d_atan.xxx d_atan.o
mv d_atan.xxx d_atan.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_atn2.c
ld -r -x -o d_atn2.xxx d_atn2.o
mv d_atn2.xxx d_atn2.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_cnjg.c
ld -r -x -o d_cnjg.xxx d_cnjg.o
mv d_cnjg.xxx d_cnjg.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_cos.c
ld -r -x -o d_cos.xxx d_cos.o
mv d_cos.xxx d_cos.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_cosh.c
ld -r -x -o d_cosh.xxx d_cosh.o
mv d_cosh.xxx d_cosh.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_dim.c
ld -r -x -o d_dim.xxx d_dim.o
mv d_dim.xxx d_dim.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_exp.c
ld -r -x -o d_exp.xxx d_exp.o
mv d_exp.xxx d_exp.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_imag.c
ld -r -x -o d_imag.xxx d_imag.o
mv d_imag.xxx d_imag.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_int.c
ld -r -x -o d_int.xxx d_int.o
mv d_int.xxx d_int.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_lg10.c
ld -r -x -o d_lg10.xxx d_lg10.o
mv d_lg10.xxx d_lg10.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_log.c
ld -r -x -o d_log.xxx d_log.o
mv d_log.xxx d_log.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_mod.c
ld -r -x -o d_mod.xxx d_mod.o
mv d_mod.xxx d_mod.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_nint.c
ld -r -x -o d_nint.xxx d_nint.o
mv d_nint.xxx d_nint.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_prod.c
ld -r -x -o d_prod.xxx d_prod.o
mv d_prod.xxx d_prod.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_sign.c
ld -r -x -o d_sign.xxx d_sign.o
mv d_sign.xxx d_sign.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_sin.c
ld -r -x -o d_sin.xxx d_sin.o
mv d_sin.xxx d_sin.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_sinh.c
ld -r -x -o d_sinh.xxx d_sinh.o
mv d_sinh.xxx d_sinh.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_sqrt.c
ld -r -x -o d_sqrt.xxx d_sqrt.o
mv d_sqrt.xxx d_sqrt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_tan.c
ld -r -x -o d_tan.xxx d_tan.o
mv d_tan.xxx d_tan.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic d_tanh.c
ld -r -x -o d_tanh.xxx d_tanh.o
mv d_tanh.xxx d_tanh.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic i_abs.c
ld -r -x -o i_abs.xxx i_abs.o
mv i_abs.xxx i_abs.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic i_dim.c
ld -r -x -o i_dim.xxx i_dim.o
mv i_dim.xxx i_dim.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic i_dnnt.c
ld -r -x -o i_dnnt.xxx i_dnnt.o
mv i_dnnt.xxx i_dnnt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic i_indx.c
ld -r -x -o i_indx.xxx i_indx.o
mv i_indx.xxx i_indx.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic i_len.c
ld -r -x -o i_len.xxx i_len.o
mv i_len.xxx i_len.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic i_mod.c
ld -r -x -o i_mod.xxx i_mod.o
mv i_mod.xxx i_mod.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic i_nint.c
ld -r -x -o i_nint.xxx i_nint.o
mv i_nint.xxx i_nint.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic i_sign.c
ld -r -x -o i_sign.xxx i_sign.o
mv i_sign.xxx i_sign.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic lbitbits.c
ld -r -x -o lbitbits.xxx lbitbits.o
mv lbitbits.xxx lbitbits.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic lbitshft.c
ld -r -x -o lbitshft.xxx lbitshft.o
mv lbitshft.xxx lbitshft.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic h_abs.c
ld -r -x -o h_abs.xxx h_abs.o
mv h_abs.xxx h_abs.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic h_dim.c
ld -r -x -o h_dim.xxx h_dim.o
mv h_dim.xxx h_dim.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic h_dnnt.c
ld -r -x -o h_dnnt.xxx h_dnnt.o
mv h_dnnt.xxx h_dnnt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic h_indx.c
ld -r -x -o h_indx.xxx h_indx.o
mv h_indx.xxx h_indx.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic h_len.c
ld -r -x -o h_len.xxx h_len.o
mv h_len.xxx h_len.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic h_mod.c
ld -r -x -o h_mod.xxx h_mod.o
mv h_mod.xxx h_mod.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic h_nint.c
ld -r -x -o h_nint.xxx h_nint.o
mv h_nint.xxx h_nint.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic h_sign.c
ld -r -x -o h_sign.xxx h_sign.o
mv h_sign.xxx h_sign.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic l_ge.c
ld -r -x -o l_ge.xxx l_ge.o
mv l_ge.xxx l_ge.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic l_gt.c
ld -r -x -o l_gt.xxx l_gt.o
mv l_gt.xxx l_gt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic l_le.c
ld -r -x -o l_le.xxx l_le.o
mv l_le.xxx l_le.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic l_lt.c
ld -r -x -o l_lt.xxx l_lt.o
mv l_lt.xxx l_lt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic hl_ge.c
ld -r -x -o hl_ge.xxx hl_ge.o
mv hl_ge.xxx hl_ge.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic hl_gt.c
ld -r -x -o hl_gt.xxx hl_gt.o
mv hl_gt.xxx hl_gt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic hl_le.c
ld -r -x -o hl_le.xxx hl_le.o
mv hl_le.xxx hl_le.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic hl_lt.c
ld -r -x -o hl_lt.xxx hl_lt.o
mv hl_lt.xxx hl_lt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic ef1asc_.c
ld -r -x -o ef1asc_.xxx ef1asc_.o
mv ef1asc_.xxx ef1asc_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic ef1cmc_.c
ld -r -x -o ef1cmc_.xxx ef1cmc_.o
mv ef1cmc_.xxx ef1cmc_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic f77_aloc.c
ld -r -x -o f77_aloc.xxx f77_aloc.o
mv f77_aloc.xxx f77_aloc.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic s_cat.c
ld -r -x -o s_cat.xxx s_cat.o
mv s_cat.xxx s_cat.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic s_cmp.c
ld -r -x -o s_cmp.xxx s_cmp.o
mv s_cmp.xxx s_cmp.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic s_copy.c
ld -r -x -o s_copy.xxx s_copy.o
mv s_copy.xxx s_copy.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic backspac.c
backspac.c: In function ‘f_back’:
backspac.c:47:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread((char *)&n,sizeof(uiolen),1,f);
^
ld -r -x -o backspac.xxx backspac.o
mv backspac.xxx backspac.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic close.c
ld -r -x -o close.xxx close.o
mv close.xxx close.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic dfe.c
ld -r -x -o dfe.xxx dfe.o
mv dfe.xxx dfe.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic dolio.c
ld -r -x -o dolio.xxx dolio.o
mv dolio.xxx dolio.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic due.c
ld -r -x -o due.xxx due.o
mv due.xxx due.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic endfile.c
ld -r -x -o endfile.xxx endfile.o
mv endfile.xxx endfile.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic err.c
ld -r -x -o err.xxx err.o
mv err.xxx err.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic fmt.c
ld -r -x -o fmt.xxx fmt.o
mv fmt.xxx fmt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic fmtlib.c
ld -r -x -o fmtlib.xxx fmtlib.o
mv fmtlib.xxx fmtlib.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic ftell_.c
ld -r -x -o ftell_.xxx ftell_.o
mv ftell_.xxx ftell_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic iio.c
ld -r -x -o iio.xxx iio.o
mv iio.xxx iio.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic ilnw.c
ld -r -x -o ilnw.xxx ilnw.o
mv ilnw.xxx ilnw.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic inquire.c
ld -r -x -o inquire.xxx inquire.o
mv inquire.xxx inquire.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic lread.c
ld -r -x -o lread.xxx lread.o
mv lread.xxx lread.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic lwrite.c
ld -r -x -o lwrite.xxx lwrite.o
mv lwrite.xxx lwrite.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic open.c
ld -r -x -o open.xxx open.o
mv open.xxx open.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic rdfmt.c
ld -r -x -o rdfmt.xxx rdfmt.o
mv rdfmt.xxx rdfmt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic rewind.c
ld -r -x -o rewind.xxx rewind.o
mv rewind.xxx rewind.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic rsfe.c
ld -r -x -o rsfe.xxx rsfe.o
mv rsfe.xxx rsfe.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic rsli.c
ld -r -x -o rsli.xxx rsli.o
mv rsli.xxx rsli.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic rsne.c
ld -r -x -o rsne.xxx rsne.o
mv rsne.xxx rsne.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic sfe.c
ld -r -x -o sfe.xxx sfe.o
mv sfe.xxx sfe.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic sue.c
ld -r -x -o sue.xxx sue.o
mv sue.xxx sue.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic typesize.c
ld -r -x -o typesize.xxx typesize.o
mv typesize.xxx typesize.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic uio.c
ld -r -x -o uio.xxx uio.o
mv uio.xxx uio.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic util.c
ld -r -x -o util.xxx util.o
mv util.xxx util.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic wref.c
ld -r -x -o wref.xxx wref.o
mv wref.xxx wref.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic wrtfmt.c
ld -r -x -o wrtfmt.xxx wrtfmt.o
mv wrtfmt.xxx wrtfmt.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic wsfe.c
ld -r -x -o wsfe.xxx wsfe.o
mv wsfe.xxx wsfe.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic wsle.c
ld -r -x -o wsle.xxx wsle.o
mv wsle.xxx wsle.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic wsne.c
ld -r -x -o wsne.xxx wsne.o
mv wsne.xxx wsne.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic xwsne.c
ld -r -x -o xwsne.xxx xwsne.o
mv xwsne.xxx xwsne.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic dtime_.c
ld -r -x -o dtime_.xxx dtime_.o
mv dtime_.xxx dtime_.o
gcc -std=gnu99 -c -DSkip_f2c_Undefs -g -O2 -fpic etime_.c
ld -r -x -o etime_.xxx etime_.o
mv etime_.xxx etime_.o
ar r libf2c.a f77vers.o i77vers.o main.o s_rnge.o abort_.o exit_.o getarg_.o iargc_.o getenv_.o signal_.o s_stop.o s_paus.o system_.o cabs.o ctype.o derf_.o derfc_.o erf_.o erfc_.o sig_die.o uninit.o pow_ci.o pow_dd.o pow_di.o pow_hh.o pow_ii.o pow_ri.o pow_zi.o pow_zz.o c_abs.o c_cos.o c_div.o c_exp.o c_log.o c_sin.o c_sqrt.o z_abs.o z_cos.o z_div.o z_exp.o z_log.o z_sin.o z_sqrt.o r_abs.o r_acos.o r_asin.o r_atan.o r_atn2.o r_cnjg.o r_cos.o r_cosh.o r_dim.o r_exp.o r_imag.o r_int.o r_lg10.o r_log.o r_mod.o r_nint.o r_sign.o r_sin.o r_sinh.o r_sqrt.o r_tan.o r_tanh.o d_abs.o d_acos.o d_asin.o d_atan.o d_atn2.o d_cnjg.o d_cos.o d_cosh.o d_dim.o d_exp.o d_imag.o d_int.o d_lg10.o d_log.o d_mod.o d_nint.o d_prod.o d_sign.o d_sin.o d_sinh.o d_sqrt.o d_tan.o d_tanh.o i_abs.o i_dim.o i_dnnt.o i_indx.o i_len.o i_mod.o i_nint.o i_sign.o lbitbits.o lbitshft.o h_abs.o h_dim.o h_dnnt.o h_indx.o h_len.o h_mod.o h_nint.o h_sign.o l_ge.o l_gt.o l_le.o l_lt.o hl_ge.o hl_gt.o hl_le.o hl_lt.o ef1asc_.o ef1cmc_.o f77_aloc.o s_cat.o s_cmp.o s_copy.o backspac.o close.o dfe.o dolio.o due.o endfile.o err.o fmt.o fmtlib.o ftell_.o iio.o ilnw.o inquire.o lread.o lwrite.o open.o rdfmt.o rewind.o rsfe.o rsli.o rsne.o sfe.o sue.o typesize.o uio.o util.o wref.o wrtfmt.o wsfe.o wsle.o wsne.o xwsne.o dtime_.o etime_.o
ar: creating libf2c.a
ranlib libf2c.a
make[1]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/eiR.Rcheck/00_pkg_src/eiR/src/f2c'
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o eiR.so apost.o char_bit_cnt.o embedCoords.o eucsearch.o format.o mplsh-model.o mplsh.o profiling.o r_wrap.o recordfile.o routines.o scan.o search_r.o solver.o -lm -Lf2c -lf2c -L. -lgsl -lgslcblas -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/eiR.Rcheck/eiR/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 (eiR)