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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Harshlight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Harshlight_1.78.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Harshlight.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Harshlight/DESCRIPTION’ ... OK
* this is package ‘Harshlight’ version ‘1.78.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  Harshlight.c:93:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Harshlight.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP:
   .C("cluster_defects", img <- as.integer(img), array.size <- as.integer(array.size), 
       as.integer(size.limit), as.integer(connect), as.double(simul.pval), 
       as.double(compact.pval), as.integer(type), status <- as.integer(0), 
       DUP = FALSE, PACKAGE = "Harshlight")
   .C("diffuse_defects", img <- as.double(img), as.double(diffuse.bright), 
       as.double(-diffuse.dark), as.integer(radius), diff.bright <- as.double(diff.bright), 
       diff.dark <- as.double(diff.dark), as.double(quant), as.double(thres.dark), 
       as.double(thres.bright), status <- as.integer(0), DUP = FALSE, 
       NAOK = TRUE, PACKAGE = "Harshlight")
   .C("extended_defects", as.double(img), med.obs <- as.double(med.obs), 
       as.integer(radius), status <- as.integer(0), NAOK = TRUE, 
       DUP = FALSE, PACKAGE = "Harshlight")
   .C("image_dilation", as.double(img), result <- as.double(result), 
       as.integer(radius), status <- as.integer(0), DUP = FALSE, 
       PACKAGE = "Harshlight")
   .C("image_erosion", as.double(result), img <- as.double(img), 
       as.integer(radius), status <- as.integer(0), DUP = FALSE, 
       PACKAGE = "Harshlight")
   .C("simulations", simulation.bright <- as.integer(simulation.bright), 
       as.double(compact.quant.bright), as.integer(compact.connect), 
       status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight")
   .C("simulations", simulation.dark <- as.integer(simulation.dark), 
       as.double(compact.quant.dark), as.integer(compact.connect), 
       status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
Harshlight: no visible binding for global variable ‘sim’
Harshlight: no visible binding for global variable ‘sim.int’
Undefined global functions or variables:
  sim sim.int
* checking Rd files ... NOTE
checkRd: (-1) sim.Rd:10: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Harshlight/libs/Harshlight.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand’, possibly from ‘srand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Harshlight.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Harshlight
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘Harshlight’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Harshlight.c -o Harshlight.o
Harshlight.c:564:20: warning: variable 'p_num_points' set but not used [-Wunused-but-set-variable]
  int num_points, *p_num_points; //number of points inside the median kernel
                   ^
Harshlight.c:789:7: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
  int counter = 0; //counter
      ^
Harshlight.c:948:10: warning: variable 'cell_value' set but not used [-Wunused-but-set-variable]
  double cell_value;
         ^
Harshlight.c:1316:27: warning: unused variable 'sorted2' [-Wunused-variable]
  double *sorted; double *sorted2;
                          ^
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:93:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
void chip_overall_header(); //general header for a chip
     ^
Harshlight.c:1504:6: note: conflicting prototype is here
void chip_overall_header(int *chip_number, char **chip_name){
     ^
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);
                                                                                                         ~^
11 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Harshlight.so Harshlight.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-Harshlight/00new/Harshlight/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Harshlight)