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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings eiR_1.14.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/eiR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.14.1’
* 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 ... 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 ... 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
IddbVsIddbDist : process : <anonymous> : <anonymous>: no visible global
function definition for ‘read.table’
checkEmbedding : embedJob: no visible global function definition for
‘head’
checkEmbedding: no visible global function definition for ‘head’
eiMakeDb: no visible global function definition for ‘str’
eiMakeDb: no visible global function definition for ‘read.table’
eiMakeDb: no visible global function definition for ‘cmdscale’
eiMakeDb: no visible global function definition for ‘write.table’
eiPerformanceTest: no visible global function definition for
‘write.table’
embedFromRefs: no visible global function definition for ‘read.table’
evaluator : <anonymous>: no visible global function definition for
‘write.table’
evaluator: no visible global function definition for ‘write.csv’
getCoords: no visible global function definition for ‘read.table’
getEmbeddedDescriptors: no visible global function definition for
‘aggregate’
insertEmbeddedDescriptors: no visible global function definition for
‘postgresqlWriteTable’
insertEmbeddedDescriptorsByCompoundId: no visible global function
definition for ‘postgresqlWriteTable’
insertGroupMembers: no visible global function definition for
‘postgresqlWriteTable’
toFile : write: no visible global function definition for ‘write.table’
toFile : writePart: no visible global function definition for
‘write.table’
writeIddbFile: no visible global function definition for ‘write.table’
Undefined global functions or variables:
aggregate cmdscale head postgresqlWriteTable read.table str write.csv
write.table
Consider adding
importFrom("stats", "aggregate", "cmdscale")
importFrom("utils", "head", "read.table", "str", "write.csv",
"write.table")
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 ... 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
eiPerformanceTest 5.732 0.168 5.908
eiCluster 5.364 0.196 5.570
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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, 6 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/eiR.Rcheck/00check.log’
for details.
* installing *source* package ‘eiR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c apost.cpp -o apost.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c char_bit_cnt.cpp -o char_bit_cnt.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c embedCoords.cc -o embedCoords.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c eucsearch.cc -o eucsearch.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c format.cc -o format.o
format.cc: In function ‘int binaryCoord(char*, char*, int)’:
format.cc:54:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i = 0; i < dim; i ++) {
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c mplsh-model.cpp -o mplsh-model.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c mplsh.cpp -o mplsh.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c profiling.cc -o profiling.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c r_wrap.cpp -o r_wrap.o
r_wrap.cpp: In function ‘SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)’:
r_wrap.cpp:948:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
const char *p = typeName;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c recordfile.cc -o recordfile.o
recordfile.cc: In function ‘int read_file(const char*, int&, std::vector<double>&, std::vector<int>&, bool)’:
recordfile.cc:45:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < dim; j ++)
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -fpic -g -O2 -Wall -c routines.c -o routines.o
routines.c: In function ‘setulb_’:
routines.c:40:28: warning: variable ‘l3’ set but not used [-Wunused-but-set-variable]
static integer l1, l2, l3, ld, lr, lt, lz, lwa, lsg, lyg, lwn, lss, lws,
^
routines.c:40:24: warning: variable ‘l2’ set but not used [-Wunused-but-set-variable]
static integer l1, l2, l3, ld, lr, lt, lz, lwa, lsg, lyg, lwn, lss, lws,
^
routines.c:40:20: warning: variable ‘l1’ set but not used [-Wunused-but-set-variable]
static integer l1, l2, l3, ld, lr, lt, lz, lwa, lsg, lyg, lwn, lss, lws,
^
routines.c: In function ‘dcsrch_’:
routines.c:4465:16: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
if (brackt && (*stp <= stmin || *stp >= stmax) || brackt && stmax - stmin
^
routines.c: In function ‘timer_’:
routines.c:4776:17: warning: variable ‘temp’ set but not used [-Wunused-but-set-variable]
static real temp;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c scan.cc -o scan.o
scan.cc: In function ‘int eucsearch(const char*, const char*, int, std::ostream&)’:
scan.cc:54:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (n_results > results.size()) n_results = results.size();
^
scan.cc:56:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i = 0; i < n_results; i ++)
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c search_r.cpp -o search_r.o
search_r.cpp: In function ‘int loadIndex(Index&, lshkit::FloatMatrix&, std::__cxx11::string&, float, unsigned int, unsigned int, unsigned int)’:
search_r.cpp:77:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned i = 0; i < data.getSize(); ++i)
^
search_r.cpp: In function ‘SEXPREC* lshsearchAll(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
search_r.cpp:146:16: warning: unused variable ‘cnt’ [-Wunused-variable]
unsigned cnt;
^
search_r.cpp:142:8: warning: unused variable ‘k’ [-Wunused-variable]
int k=0;
^
search_r.cpp: In function ‘SEXPREC* query(SEXP, SEXP, SEXP, SEXP, SEXP)’:
search_r.cpp:273:16: warning: unused variable ‘cnt’ [-Wunused-variable]
unsigned cnt;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -Iinclude -I. -fpic -g -O2 -Wall -c solver.cc -o solver.o
solver.cc: In destructor ‘Solver::˜Solver()’:
solver.cc:38:12: warning: right operand of comma operator has no effect [-Wunused-value]
delete p, nbd, iwa, l, u, g, wa;
^
solver.cc:38:17: warning: right operand of comma operator has no effect [-Wunused-value]
delete p, nbd, iwa, l, u, g, wa;
^
solver.cc:38:22: warning: right operand of comma operator has no effect [-Wunused-value]
delete p, nbd, iwa, l, u, g, wa;
^
solver.cc:38:25: warning: right operand of comma operator has no effect [-Wunused-value]
delete p, nbd, iwa, l, u, g, wa;
^
solver.cc:38:28: warning: right operand of comma operator has no effect [-Wunused-value]
delete p, nbd, iwa, l, u, g, wa;
^
solver.cc:38:31: warning: right operand of comma operator has no effect [-Wunused-value]
delete p, nbd, iwa, l, u, g, wa;
^
solver.cc: In member function ‘int Solver::optim(doublereal*, doublereal*, doublereal, doublereal)’:
solver.cc:91:7: warning: unused variable ‘buf’ [-Wunused-variable]
char buf[60] = "";
^
make[1]: Entering directory '/home/biocbuild/bbs-3.4-bioc/meat/eiR.Rcheck/00_pkg_src/eiR/src/f2c'
cp signal1.h0 signal1.h
cp sysdep1.h0 sysdep1.h
gcc -c f77vers.c
gcc -c i77vers.c
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic main.c
main.c:56:13: warning: ‘sigfdie’ defined but not used [-Wunused-function]
static VOID sigfdie(Sigarg)
^
main.c:63:13: warning: ‘sigidie’ defined but not used [-Wunused-function]
static VOID sigidie(Sigarg)
^
main.c:70:13: warning: ‘sigqdie’ defined but not used [-Wunused-function]
static VOID sigqdie(Sigarg)
^
main.c:78:13: warning: ‘sigindie’ defined but not used [-Wunused-function]
static VOID sigindie(Sigarg)
^
main.c:84:13: warning: ‘sigtdie’ defined but not used [-Wunused-function]
static VOID sigtdie(Sigarg)
^
main.c:91:13: warning: ‘sigtrdie’ defined but not used [-Wunused-function]
static VOID sigtrdie(Sigarg)
^
ld -r -x -o main.xxx main.o
mv main.xxx main.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic s_rnge.c
ld -r -x -o s_rnge.xxx s_rnge.o
mv s_rnge.xxx s_rnge.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic abort_.c
ld -r -x -o abort_.xxx abort_.o
mv abort_.xxx abort_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic exit_.c
ld -r -x -o exit_.xxx exit_.o
mv exit_.xxx exit_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic getarg_.c
ld -r -x -o getarg_.xxx getarg_.o
mv getarg_.xxx getarg_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic iargc_.c
ld -r -x -o iargc_.xxx iargc_.o
mv iargc_.xxx iargc_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic getenv_.c
ld -r -x -o getenv_.xxx getenv_.o
mv getenv_.xxx getenv_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic signal_.c
ld -r -x -o signal_.xxx signal_.o
mv signal_.xxx signal_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic s_stop.c
ld -r -x -o s_stop.xxx s_stop.o
mv s_stop.xxx s_stop.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic s_paus.c
s_paus.c:29:1: warning: ‘waitpause’ defined but not used [-Wunused-function]
waitpause(Sigarg)
^
s_paus.c:39:1: warning: ‘s_1paus’ defined but not used [-Wunused-function]
s_1paus(FILE *fin)
^
ld -r -x -o s_paus.xxx s_paus.o
mv s_paus.xxx s_paus.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic system_.c
ld -r -x -o system_.xxx system_.o
mv system_.xxx system_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic cabs.c
ld -r -x -o cabs.xxx cabs.o
mv cabs.xxx cabs.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic ctype.c
ld -r -x -o ctype.xxx ctype.o
mv ctype.xxx ctype.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic derf_.c
ld -r -x -o derf_.xxx derf_.o
mv derf_.xxx derf_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic derfc_.c
ld -r -x -o derfc_.xxx derfc_.o
mv derfc_.xxx derfc_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic erf_.c
ld -r -x -o erf_.xxx erf_.o
mv erf_.xxx erf_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic erfc_.c
ld -r -x -o erfc_.xxx erfc_.o
mv erfc_.xxx erfc_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic sig_die.c
ld -r -x -o sig_die.xxx sig_die.o
mv sig_die.xxx sig_die.o
gcc -o a.out -g -O2 -Wall -fpic -DNO_FPINIT arithchk.c -lm ||\
gcc -o a.out -DNO_LONG_LONG -g -O2 -Wall -fpic -DNO_FPINIT arithchk.c -lm
arithchk.c: In function ‘need_nancheck’:
arithchk.c:158:9: warning: variable ‘t’ set but not used [-Wunused-but-set-variable]
double t;
^
./a.out >arith.h
rm -f a.out arithchk.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic uninit.c
ld -r -x -o uninit.xxx uninit.o
mv uninit.xxx uninit.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic pow_ci.c
ld -r -x -o pow_ci.xxx pow_ci.o
mv pow_ci.xxx pow_ci.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic pow_dd.c
ld -r -x -o pow_dd.xxx pow_dd.o
mv pow_dd.xxx pow_dd.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic pow_di.c
ld -r -x -o pow_di.xxx pow_di.o
mv pow_di.xxx pow_di.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic pow_hh.c
ld -r -x -o pow_hh.xxx pow_hh.o
mv pow_hh.xxx pow_hh.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic pow_ii.c
ld -r -x -o pow_ii.xxx pow_ii.o
mv pow_ii.xxx pow_ii.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic pow_ri.c
ld -r -x -o pow_ri.xxx pow_ri.o
mv pow_ri.xxx pow_ri.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic pow_zi.c
ld -r -x -o pow_zi.xxx pow_zi.o
mv pow_zi.xxx pow_zi.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic pow_zz.c
ld -r -x -o pow_zz.xxx pow_zz.o
mv pow_zz.xxx pow_zz.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic c_abs.c
ld -r -x -o c_abs.xxx c_abs.o
mv c_abs.xxx c_abs.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic c_cos.c
ld -r -x -o c_cos.xxx c_cos.o
mv c_cos.xxx c_cos.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic c_div.c
ld -r -x -o c_div.xxx c_div.o
mv c_div.xxx c_div.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic c_exp.c
ld -r -x -o c_exp.xxx c_exp.o
mv c_exp.xxx c_exp.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic c_log.c
ld -r -x -o c_log.xxx c_log.o
mv c_log.xxx c_log.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic c_sin.c
ld -r -x -o c_sin.xxx c_sin.o
mv c_sin.xxx c_sin.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic c_sqrt.c
ld -r -x -o c_sqrt.xxx c_sqrt.o
mv c_sqrt.xxx c_sqrt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic z_abs.c
ld -r -x -o z_abs.xxx z_abs.o
mv z_abs.xxx z_abs.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic z_cos.c
ld -r -x -o z_cos.xxx z_cos.o
mv z_cos.xxx z_cos.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic z_div.c
ld -r -x -o z_div.xxx z_div.o
mv z_div.xxx z_div.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic z_exp.c
ld -r -x -o z_exp.xxx z_exp.o
mv z_exp.xxx z_exp.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic z_log.c
ld -r -x -o z_log.xxx z_log.o
mv z_log.xxx z_log.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic z_sin.c
ld -r -x -o z_sin.xxx z_sin.o
mv z_sin.xxx z_sin.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic z_sqrt.c
ld -r -x -o z_sqrt.xxx z_sqrt.o
mv z_sqrt.xxx z_sqrt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_abs.c
ld -r -x -o r_abs.xxx r_abs.o
mv r_abs.xxx r_abs.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_acos.c
ld -r -x -o r_acos.xxx r_acos.o
mv r_acos.xxx r_acos.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_asin.c
ld -r -x -o r_asin.xxx r_asin.o
mv r_asin.xxx r_asin.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_atan.c
ld -r -x -o r_atan.xxx r_atan.o
mv r_atan.xxx r_atan.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_atn2.c
ld -r -x -o r_atn2.xxx r_atn2.o
mv r_atn2.xxx r_atn2.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_cnjg.c
ld -r -x -o r_cnjg.xxx r_cnjg.o
mv r_cnjg.xxx r_cnjg.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_cos.c
ld -r -x -o r_cos.xxx r_cos.o
mv r_cos.xxx r_cos.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_cosh.c
ld -r -x -o r_cosh.xxx r_cosh.o
mv r_cosh.xxx r_cosh.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_dim.c
ld -r -x -o r_dim.xxx r_dim.o
mv r_dim.xxx r_dim.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_exp.c
ld -r -x -o r_exp.xxx r_exp.o
mv r_exp.xxx r_exp.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_imag.c
ld -r -x -o r_imag.xxx r_imag.o
mv r_imag.xxx r_imag.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_int.c
ld -r -x -o r_int.xxx r_int.o
mv r_int.xxx r_int.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_lg10.c
ld -r -x -o r_lg10.xxx r_lg10.o
mv r_lg10.xxx r_lg10.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_log.c
ld -r -x -o r_log.xxx r_log.o
mv r_log.xxx r_log.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_mod.c
ld -r -x -o r_mod.xxx r_mod.o
mv r_mod.xxx r_mod.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_nint.c
ld -r -x -o r_nint.xxx r_nint.o
mv r_nint.xxx r_nint.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_sign.c
ld -r -x -o r_sign.xxx r_sign.o
mv r_sign.xxx r_sign.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_sin.c
ld -r -x -o r_sin.xxx r_sin.o
mv r_sin.xxx r_sin.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_sinh.c
ld -r -x -o r_sinh.xxx r_sinh.o
mv r_sinh.xxx r_sinh.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_sqrt.c
ld -r -x -o r_sqrt.xxx r_sqrt.o
mv r_sqrt.xxx r_sqrt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_tan.c
ld -r -x -o r_tan.xxx r_tan.o
mv r_tan.xxx r_tan.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic r_tanh.c
ld -r -x -o r_tanh.xxx r_tanh.o
mv r_tanh.xxx r_tanh.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_abs.c
ld -r -x -o d_abs.xxx d_abs.o
mv d_abs.xxx d_abs.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_acos.c
ld -r -x -o d_acos.xxx d_acos.o
mv d_acos.xxx d_acos.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_asin.c
ld -r -x -o d_asin.xxx d_asin.o
mv d_asin.xxx d_asin.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_atan.c
ld -r -x -o d_atan.xxx d_atan.o
mv d_atan.xxx d_atan.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_atn2.c
ld -r -x -o d_atn2.xxx d_atn2.o
mv d_atn2.xxx d_atn2.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_cnjg.c
ld -r -x -o d_cnjg.xxx d_cnjg.o
mv d_cnjg.xxx d_cnjg.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_cos.c
ld -r -x -o d_cos.xxx d_cos.o
mv d_cos.xxx d_cos.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_cosh.c
ld -r -x -o d_cosh.xxx d_cosh.o
mv d_cosh.xxx d_cosh.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_dim.c
ld -r -x -o d_dim.xxx d_dim.o
mv d_dim.xxx d_dim.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_exp.c
ld -r -x -o d_exp.xxx d_exp.o
mv d_exp.xxx d_exp.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_imag.c
ld -r -x -o d_imag.xxx d_imag.o
mv d_imag.xxx d_imag.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_int.c
ld -r -x -o d_int.xxx d_int.o
mv d_int.xxx d_int.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_lg10.c
ld -r -x -o d_lg10.xxx d_lg10.o
mv d_lg10.xxx d_lg10.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_log.c
ld -r -x -o d_log.xxx d_log.o
mv d_log.xxx d_log.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_mod.c
ld -r -x -o d_mod.xxx d_mod.o
mv d_mod.xxx d_mod.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_nint.c
ld -r -x -o d_nint.xxx d_nint.o
mv d_nint.xxx d_nint.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_prod.c
ld -r -x -o d_prod.xxx d_prod.o
mv d_prod.xxx d_prod.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_sign.c
ld -r -x -o d_sign.xxx d_sign.o
mv d_sign.xxx d_sign.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_sin.c
ld -r -x -o d_sin.xxx d_sin.o
mv d_sin.xxx d_sin.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_sinh.c
ld -r -x -o d_sinh.xxx d_sinh.o
mv d_sinh.xxx d_sinh.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_sqrt.c
ld -r -x -o d_sqrt.xxx d_sqrt.o
mv d_sqrt.xxx d_sqrt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_tan.c
ld -r -x -o d_tan.xxx d_tan.o
mv d_tan.xxx d_tan.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic d_tanh.c
ld -r -x -o d_tanh.xxx d_tanh.o
mv d_tanh.xxx d_tanh.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic i_abs.c
ld -r -x -o i_abs.xxx i_abs.o
mv i_abs.xxx i_abs.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic i_dim.c
ld -r -x -o i_dim.xxx i_dim.o
mv i_dim.xxx i_dim.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic i_dnnt.c
ld -r -x -o i_dnnt.xxx i_dnnt.o
mv i_dnnt.xxx i_dnnt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic i_indx.c
ld -r -x -o i_indx.xxx i_indx.o
mv i_indx.xxx i_indx.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic i_len.c
ld -r -x -o i_len.xxx i_len.o
mv i_len.xxx i_len.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic i_mod.c
ld -r -x -o i_mod.xxx i_mod.o
mv i_mod.xxx i_mod.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic i_nint.c
ld -r -x -o i_nint.xxx i_nint.o
mv i_nint.xxx i_nint.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic i_sign.c
ld -r -x -o i_sign.xxx i_sign.o
mv i_sign.xxx i_sign.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic lbitbits.c
lbitbits.c: In function ‘lbit_cshift’:
lbitbits.c:47:44: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
return (integer)(x << b | x >> LONGBITS -b );
^
lbitbits.c:51:34: warning: suggest parentheses around ‘-’ inside ‘<<’ [-Wparentheses]
return (integer)(x << LONGBITS - b | x >> b);
^
lbitbits.c:60:47: warning: suggest parentheses around ‘-’ inside ‘>>’ [-Wparentheses]
return (integer)(y | z & (x << b | x >> len - b));
^
lbitbits.c:60:26: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
return (integer)(y | z & (x << b | x >> len - b));
^
lbitbits.c:64:46: warning: suggest parentheses around ‘-’ inside ‘<<’ [-Wparentheses]
return (integer)(y | z & (x >> b | x << len - b));
^
lbitbits.c:64:25: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
return (integer)(y | z & (x >> b | x << len - b));
^
ld -r -x -o lbitbits.xxx lbitbits.o
mv lbitbits.xxx lbitbits.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic lbitshft.c
ld -r -x -o lbitshft.xxx lbitshft.o
mv lbitshft.xxx lbitshft.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic h_abs.c
ld -r -x -o h_abs.xxx h_abs.o
mv h_abs.xxx h_abs.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic h_dim.c
ld -r -x -o h_dim.xxx h_dim.o
mv h_dim.xxx h_dim.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic h_dnnt.c
ld -r -x -o h_dnnt.xxx h_dnnt.o
mv h_dnnt.xxx h_dnnt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic h_indx.c
ld -r -x -o h_indx.xxx h_indx.o
mv h_indx.xxx h_indx.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic h_len.c
ld -r -x -o h_len.xxx h_len.o
mv h_len.xxx h_len.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic h_mod.c
ld -r -x -o h_mod.xxx h_mod.o
mv h_mod.xxx h_mod.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic h_nint.c
ld -r -x -o h_nint.xxx h_nint.o
mv h_nint.xxx h_nint.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic h_sign.c
ld -r -x -o h_sign.xxx h_sign.o
mv h_sign.xxx h_sign.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic l_ge.c
ld -r -x -o l_ge.xxx l_ge.o
mv l_ge.xxx l_ge.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic l_gt.c
ld -r -x -o l_gt.xxx l_gt.o
mv l_gt.xxx l_gt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic l_le.c
ld -r -x -o l_le.xxx l_le.o
mv l_le.xxx l_le.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic l_lt.c
ld -r -x -o l_lt.xxx l_lt.o
mv l_lt.xxx l_lt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic hl_ge.c
ld -r -x -o hl_ge.xxx hl_ge.o
mv hl_ge.xxx hl_ge.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic hl_gt.c
ld -r -x -o hl_gt.xxx hl_gt.o
mv hl_gt.xxx hl_gt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic hl_le.c
ld -r -x -o hl_le.xxx hl_le.o
mv hl_le.xxx hl_le.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic hl_lt.c
ld -r -x -o hl_lt.xxx hl_lt.o
mv hl_lt.xxx hl_lt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic ef1asc_.c
ld -r -x -o ef1asc_.xxx ef1asc_.o
mv ef1asc_.xxx ef1asc_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic ef1cmc_.c
ld -r -x -o ef1cmc_.xxx ef1cmc_.o
mv ef1cmc_.xxx ef1cmc_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic f77_aloc.c
ld -r -x -o f77_aloc.xxx f77_aloc.o
mv f77_aloc.xxx f77_aloc.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic s_cat.c
ld -r -x -o s_cat.xxx s_cat.o
mv s_cat.xxx s_cat.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic s_cmp.c
ld -r -x -o s_cmp.xxx s_cmp.o
mv s_cmp.xxx s_cmp.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic s_copy.c
ld -r -x -o s_copy.xxx s_copy.o
mv s_copy.xxx s_copy.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic backspac.c
backspac.c: In function ‘f_back’:
backspac.c:47:3: 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 -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic close.c
ld -r -x -o close.xxx close.o
mv close.xxx close.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic dfe.c
dfe.c: In function ‘s_rdfe’:
dfe.c:104:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_dfe(a))return(n);
^
dfe.c: In function ‘s_wdfe’:
dfe.c:126:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_dfe(a)) return(n);
^
ld -r -x -o dfe.xxx dfe.o
mv dfe.xxx dfe.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic dolio.c
ld -r -x -o dolio.xxx dolio.o
mv dolio.xxx dolio.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic due.c
due.c: In function ‘s_rdue’:
due.c:40:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_due(a)) return(n);
^
due.c: In function ‘s_wdue’:
due.c:53:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_due(a)) return(n);
^
ld -r -x -o due.xxx due.o
mv due.xxx due.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic endfile.c
endfile.c: In function ‘f_end’:
endfile.c:46:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tf = FOPEN(nbuf, f__w_mode[0]))
^
ld -r -x -o endfile.xxx endfile.o
mv endfile.xxx endfile.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic err.c
ld -r -x -o err.xxx err.o
mv err.xxx err.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic fmt.c
ld -r -x -o fmt.xxx fmt.o
mv fmt.xxx fmt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic fmtlib.c
ld -r -x -o fmtlib.xxx fmtlib.o
mv fmtlib.xxx fmtlib.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic ftell_.c
ld -r -x -o ftell_.xxx ftell_.o
mv ftell_.xxx ftell_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic iio.c
iio.c: In function ‘s_rsfi’:
iio.c:91:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_si(a)) return(n);
^
iio.c: In function ‘s_wsfi’:
iio.c:123:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_si(a)) return(n);
^
ld -r -x -o iio.xxx iio.o
mv iio.xxx iio.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic ilnw.c
ld -r -x -o ilnw.xxx ilnw.o
mv ilnw.xxx ilnw.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic inquire.c
inquire.c: In function ‘f_inqu’:
inquire.c:67:13: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
if(byfile && x != -1 || !byfile && p!=NULL)
^
inquire.c:66:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->inex!=NULL)
^
inquire.c:70:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->inopen!=NULL)
^
inquire.c:75:24: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
if(byfile || p!=NULL && p->ufnm!=NULL)
^
inquire.c:74:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->innamed!=NULL)
^
inquire.c:78:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->inname!=NULL)
^
inquire.c:83:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->inacc!=NULL && p!=NULL && p->ufd!=NULL)
^
inquire.c:87:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->inseq!=NULL)
^
inquire.c:91:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->indir!=NULL)
^
inquire.c:95:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->infmt!=NULL)
^
inquire.c:99:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->inform!=NULL)
^
inquire.c:103:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->inunf)
^
inquire.c:112:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(a->inblank && p!=NULL && p->ufmt)
^
ld -r -x -o inquire.xxx inquire.o
mv inquire.xxx inquire.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic lread.c
lread.c: In function ‘l_C’:
lread.c:294:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (rd_count(ch))
^
lread.c:317:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (ch = l_R(1,0))
^
lread.c:329:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (ch = l_R(1,0))
^
lread.c: In function ‘nmL_getc’:
lread.c:356:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (rv = *nmL_next++)
^
lread.c: In function ‘l_L’:
lread.c:438:5: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(GETC(ch)!='*')
^
lread.c: In function ‘l_read’:
lread.c:693:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
ERR(l_R(0,1));
^
lread.c:698:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
ERR(l_R(0,0));
^
lread.c:709:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
ERR(l_C());
^
lread.c:714:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
ERR(l_L());
^
lread.c:717:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
ERR(l_CHAR());
^
lread.c: In function ‘s_rsle’:
lread.c:790:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_le(a)) return(n);
^
ld -r -x -o lread.xxx lread.o
mv lread.xxx lread.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic lwrite.c
lwrite.c: In function ‘l_g’:
lwrite.c:141:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while(b[0] = b[1])
^
lwrite.c:166:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
for(c1 = '.', c = 'E'; *b = c1;
^
lwrite.c: In function ‘l_put’:
lwrite.c:190:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while(c = *s++)
^
ld -r -x -o lwrite.xxx lwrite.o
mv lwrite.xxx lwrite.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic open.c
open.c: In function ‘f_open’:
open.c:246:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tf = FOPEN(buf,f__w_mode[0]))
^
open.c:256:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (tf = FOPEN(buf, f__r_mode[ufmt]))
^
open.c:258:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
else if (tf = FOPEN(buf, f__w_mode[ufmt])) {
^
open.c:270:4: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if(b->useek)
^
ld -r -x -o open.xxx open.o
mv open.xxx open.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic rdfmt.c
rdfmt.c: In function ‘rd_Z’:
rdfmt.c:39:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while(ch = *sc++)
^
rdfmt.c:42:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while(ch = *sc++)
^
rdfmt.c:71:9: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses]
w2 = w1+1 >> 1;
^
rdfmt.c:93:23: warning: suggest parentheses around ‘-’ inside ‘<<’ [-Wparentheses]
*t = hex[*s0 & 0xff]-1 << 4 | hex[s0[1] & 0xff]-1;
^
rdfmt.c:93:50: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses]
*t = hex[*s0 & 0xff]-1 << 4 | hex[s0[1] & 0xff]-1;
^
ld -r -x -o rdfmt.xxx rdfmt.o
mv rdfmt.xxx rdfmt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic rewind.c
ld -r -x -o rewind.xxx rewind.o
mv rewind.xxx rewind.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic rsfe.c
rsfe.c: In function ‘s_rsfe’:
rsfe.c:67:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_sfe(a)) return(n);
^
ld -r -x -o rsfe.xxx rsfe.o
mv rsfe.xxx rsfe.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic rsli.c
ld -r -x -o rsli.xxx rsli.o
mv rsli.xxx rsli.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic rsne.c
rsne.c: In function ‘hash’:
rsne.c:86:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
for(x = 0; c = *s++; x = x & 0x4000 ? ((x << 1) & 0x7fff) + 1 : x << 1)
^
rsne.c: In function ‘mk_hashtab’:
rsne.c:107:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
for(x = &nl_cache; y = *x; x0 = x, x = &y->next)
^
rsne.c: In function ‘nl_init’:
rsne.c:159:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
for(s = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"; c = *s++; )
^
rsne.c:165:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
for(s = "0123456789_"; c = *s++; )
^
rsne.c: In function ‘getname’:
rsne.c:188:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while(*s = Alphanum[GETC(ch) & 0xff])
^
rsne.c: In function ‘getdimen’:
rsne.c:243:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (k = getnum(chp, x1))
^
rsne.c:247:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (k = getnum(chp, &x2))
^
rsne.c:251:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (k = getnum(chp, &x3))
^
rsne.c: In function ‘x_rsne’:
rsne.c:349:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (ch = getname(buf,sizeof(buf)))
^
rsne.c:401:19: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
if (ch <= ' ' && ch >= 0 || ch == ',')
^
rsne.c:404:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (ch = getname(buf,sizeof(buf)))
^
rsne.c:429:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
(ftnlen)size, &b))
^
rsne.c:445:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (k = getdimen(&ch, dn, size, nomax, &b))
^
rsne.c:457:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
span, &b1))
^
rsne.c:476:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (k = getdimen(&ch, &substr, size, size, &b))
^
rsne.c:511:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
else if (dims = v->dims) {
^
rsne.c:531:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (k = l_read(&no1, vaddr + iva, size, type))
^
rsne.c:542:8: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
size, type))
^
rsne.c:549:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (readall)
^
rsne.c: In function ‘s_rsne’:
rsne.c:603:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n = c_le(a))
^
rsne.c: In function ‘mk_hashtab’:
rsne.c:112:5: warning: ‘x0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
y = *x0;
^
rsne.c: In function ‘x_rsne’:
rsne.c:580:8: warning: ‘dn0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (++dn1->curval < dn1->extent) {
^
rsne.c:579:4: warning: ‘dn’ may be used uninitialized in this function [-Wmaybe-uninitialized]
for(dn1 = dn0; dn1 <= dn; dn1++) {
^
ld -r -x -o rsne.xxx rsne.o
mv rsne.xxx rsne.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic sfe.c
ld -r -x -o sfe.xxx sfe.o
mv sfe.xxx sfe.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic sue.c
sue.c: In function ‘s_rsue’:
sue.c:38:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_sue(a)) return(n);
^
sue.c: In function ‘s_wsue’:
sue.c:61:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_sue(a)) return(n);
^
ld -r -x -o sue.xxx sue.o
mv sue.xxx sue.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic typesize.c
ld -r -x -o typesize.xxx typesize.o
mv typesize.xxx typesize.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic uio.c
ld -r -x -o uio.xxx uio.o
mv uio.xxx uio.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic util.c
ld -r -x -o util.xxx util.o
mv util.xxx util.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic wref.c
wref.c: In function ‘wrt_E’:
wref.c:140:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
for(s -= 2, e1 = 2; s[0] = s[1]; s++)
^
wref.c: In function ‘wrt_F’:
wref.c:236:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (n = f__scale)
^
wref.c:236:5: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (n = f__scale)
^
wref.c:286:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while(n = *b++)
^
ld -r -x -o wref.xxx wref.o
mv wref.xxx wref.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic wrtfmt.c
ld -r -x -o wrtfmt.xxx wrtfmt.o
mv wrtfmt.xxx wrtfmt.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic wsfe.c
wsfe.c: In function ‘s_wsfe’:
wsfe.c:55:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_sfe(a)) return(n);
^
ld -r -x -o wsfe.xxx wsfe.o
mv wsfe.xxx wsfe.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic wsle.c
wsle.c: In function ‘s_wsle’:
wsle.c:17:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_le(a)) return(n);
^
ld -r -x -o wsle.xxx wsle.o
mv wsle.xxx wsle.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic wsne.c
wsne.c: In function ‘s_wsne’:
wsne.c:17:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if(n=c_le(a))
^
ld -r -x -o wsne.xxx wsne.o
mv wsne.xxx wsne.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic xwsne.c
ld -r -x -o xwsne.xxx xwsne.o
mv xwsne.xxx xwsne.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -fpic dtime_.c
ld -r -x -o dtime_.xxx dtime_.o
mv dtime_.xxx dtime_.o
gcc -c -DSkip_f2c_Undefs -g -O2 -Wall -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-3.4-bioc/meat/eiR.Rcheck/00_pkg_src/eiR/src/f2c'
g++ -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)
