Harshlight 1.46.0
Maurizio Pellegrino
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Harshlight | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Harshlight_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Harshlight.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Harshlight/DESCRIPTION’ ... OK
* this is package ‘Harshlight’ version ‘1.46.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Harshlight’ can be installed ... OK
* 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 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 ... 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 ... 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 compiled code ... NOTE
File ‘Harshlight/libs/Harshlight.so’:
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Object: ‘Harshlight.o’
Found ‘_rand’, possibly from ‘rand’ (C)
Object: ‘Harshlight.o’
Found ‘_srand’, possibly from ‘srand’ (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, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/Harshlight.Rcheck/00check.log’
for details.
* installing *source* package ‘Harshlight’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Harshlight.c -o Harshlight.o
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: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);
˜^
7 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-3.4-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)