BioC 3.1: CHECK report for eiR on zin2

Package: eiR

Version: 1.8.3

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings eiR_1.8.3.tar.gz

StartedAt: 2015-10-09 00:49:44 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:52:52 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 188.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: eiR.Rcheck

Warnings: 1

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###
### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings eiR_1.8.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/eiR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.8.3’
* 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 ... [35s/62s] 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’
* 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 ... [26s/34s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
eiPerformanceTest 6.290  0.341   7.018
eiCluster         5.687  0.275  10.325
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [28s/47s]
 [28s/47s] 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-3.1-bioc/meat/eiR.Rcheck/00check.log’
for details.

* installing *source* package ‘eiR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"  -DNO_MAIN -Iinclude -I. -fpic  -g -O2  -Wall -c apost.cpp -o apost.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"  -DNO_MAIN -Iinclude -I. -fpic  -g -O2  -Wall -c embedCoords.cc -o embedCoords.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"  -DNO_MAIN -Iinclude -I. -fpic  -g -O2  -Wall -c eucsearch.cc -o eucsearch.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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:54:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i = 0; i < dim; i ++) {
                                ^
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"  -DNO_MAIN -Iinclude -I. -fpic  -g -O2  -Wall -c mplsh.cpp -o mplsh.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"  -DNO_MAIN -Iinclude -I. -fpic  -g -O2  -Wall -c profiling.cc -o profiling.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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:45:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (size_t j = 0; j < dim; j ++)
                          ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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:54:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (n_results > results.size()) n_results = results.size();
                                ^
scan.cc:56:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i = 0; i < n_results; i ++)
                                ^
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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::string&, float, unsigned int, unsigned int, unsigned int)’:
search_r.cpp:77:42: 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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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:38:17: 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:38:33: 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-3.1-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  -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 -std=gnu99 -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -fpic -DNO_FPINIT arithchk.c -lm ||\
	 gcc -std=gnu99 -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -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 -std=gnu99 -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -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)
    ^
inquire.c:67:18: warning: ‘x’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(byfile && x != -1 || !byfile && p!=NULL)
                  ^
ld -r -x -o inquire.xxx inquire.o
mv inquire.xxx inquire.o
gcc -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -Wall -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  -Wall -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  -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -c -DSkip_f2c_Undefs -g -O2  -Wall -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  -Wall -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  -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-3.1-bioc/meat/eiR.Rcheck/00_pkg_src/eiR/src/f2c'
g++ -shared -L/home/biocbuild/bbs-3.1-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-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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)

name	user	system	elapsed
addTransform	0.003	0.000	0.007
eiAdd	3.503	0.296	4.890
eiCluster	5.687	0.275	10.325
eiInit	1.859	0.029	2.401
eiMakeDb	3.057	0.268	3.612
eiPerformanceTest	6.290	0.341	7.018
eiQuery	3.287	0.315	4.614
freeLSHData	0	0	0
loadLSHData	0.001	0.000	0.000
setDefaultDistance	0.001	0.000	0.001