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Package 308/671HostnameOS / ArchBUILDCHECKBUILD BIN
Harshlight 1.32.1
Maurizio Pellegrino
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Harshlight
Last Changed Rev: 75507 / Revision: 76155
Last Changed Date: 2013-04-10 09:53:37 -0700 (Wed, 10 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: Harshlight
Version: 1.32.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Harshlight_1.32.1.tar.gz
StartedAt: 2013-05-01 06:46:12 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 06:48:51 -0700 (Wed, 01 May 2013)
EllapsedTime: 159.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Harshlight.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Harshlight.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Harshlight/DESCRIPTION' ... OK
* this is package 'Harshlight' version '1.32.1'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'Harshlight' can be installed ... [16s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Harshlight: no visible binding for global variable 'sim'
Harshlight: no visible binding for global variable 'sim.int'
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/Harshlight.Rcheck/Harshlight/libs/Harshlight.so':
  Found '___stderrp', possibly from 'stderr' (C)
    Object: 'Harshlight.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [8s/8s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/Harshlight.Rcheck/00check.log'
for details.

Harshlight.Rcheck/00install.out:

* installing *source* package 'Harshlight' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Harshlight.c -o Harshlight.o
Harshlight.c:140:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  if ((to_do_stack = malloc(to_do_alloc * sizeof(int))) == NULL){
                            ^˜˜˜˜˜˜˜˜˜˜ ˜
Harshlight.c:221:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    if ((curr_tmp = realloc(to_do_stack, (to_do_alloc + 8*max_size) * sizeof(int))) == NULL){
                                          ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜  ˜
Harshlight.c:294:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      curr_tmp = realloc(to_do_stack, (to_do_alloc + 8*max_size) * sizeof(int));
                                       ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜  ˜
Harshlight.c:587:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  if ((circle_value = (double *)malloc(num_points*sizeof(double))) == NULL){
                                       ^˜˜˜˜˜˜˜˜˜˜
Harshlight.c:1032:26: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  area = 2*3.14*r_square + 50;
       ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
Harshlight.c:1034:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  if ((*stack1 = malloc(area * sizeof(int))) == NULL){
                        ^˜˜˜ ˜
Harshlight.c:1068:26: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  area = 2*3.14*r_square + 50;
       ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
Harshlight.c:1070:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  if ((*stack1 = malloc(area * sizeof(int))) == NULL){
                        ^˜˜˜ ˜
Harshlight.c:1079:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  if ((*stack2 = malloc(area * sizeof(int))) == NULL){
                        ^˜˜˜ ˜
Harshlight.c:1124:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  if ((new_list = (double *)malloc(area_new_list*sizeof(double))) == NULL){
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜
Harshlight.c:1220:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  if ((random_list = malloc(ROW*COL * sizeof(int))) == NULL){
                            ˜˜˜^˜˜˜ ˜
Harshlight.c:1318:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  if((sorted = (double *)malloc(*size*sizeof(double))) == NULL){
                                ^˜˜˜˜˜
Harshlight.c:1316:27: warning: unused variable 'sorted2' [-Wunused-variable]
  double *sorted; double *sorted2;
                          ^
Harshlight.c:1350:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  if((sorted = (double *)malloc(*size*sizeof(double))) == NULL){
                                ^˜˜˜˜˜
Harshlight.c:1471:26: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 215, *diff_br);
                        ˜^
Harshlight.c:1474:26: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 230, *diff_dr);
                        ˜^
Harshlight.c:1532:107: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (Extended defects: the variance of the Error Image explained by the background is %.2f%) show\n", x_text, y_text - 30, *var);
                                                                                                         ˜^
Harshlight.c:1542:26: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (%.2f%) show\n", x_val_1, y_text - 100, *perc_c);
                        ˜^
Harshlight.c:1543:26: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (%.2f%) show\n", x_val_2, y_text - 100, *perc_d);
                        ˜^
Harshlight.c:1555:107: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (Extended defects: the variance of the Error Image explained by the background is %.2f%) show\n", x_text, y_text - 30, *var);
                                                                                                         ˜^
20 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o Harshlight.so Harshlight.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Harshlight.Rcheck/Harshlight/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 (Harshlight)

Harshlight.Rcheck/Harshlight-Ex.timings:

nameusersystemelapsed
Harshlight0.2770.0070.296