Maurizio Pellegrino
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Harshlight |
| Branch: RELEASE_3_8 |
| Last Commit: 277554c |
| Last Changed Date: 2018-10-30 11:41:43 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:19:58 -0400 (Sat, 13 Apr 2019).
| Package 708/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Harshlight 1.54.0 Maurizio Pellegrino
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Harshlight |
| Version: 1.54.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Harshlight.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Harshlight_1.54.0.tar.gz |
| StartedAt: 2019-04-13 02:58:46 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:01:23 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 157.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Harshlight.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Harshlight.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Harshlight_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Harshlight.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Harshlight/DESCRIPTION' ... OK
* this is package 'Harshlight' version '1.54.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/Harshlight/libs/i386/Harshlight.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
'C:/Users/biocbuild/bbs-3.8-bioc/meat/Harshlight.Rcheck/00check.log'
for details.
Harshlight.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Harshlight_1.54.0.tar.gz && rm -rf Harshlight.buildbin-libdir && mkdir Harshlight.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Harshlight.buildbin-libdir Harshlight_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Harshlight_1.54.0.zip && rm Harshlight_1.54.0.tar.gz Harshlight_1.54.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 101k 100 101k 0 0 2364k 0 --:--:-- --:--:-- --:--:-- 2610k
install for i386
* installing *source* package 'Harshlight' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Harshlight.c -o Harshlight.o
Harshlight.c: In function 'extended_defects':
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: In function 'image_dilation':
Harshlight.c:948:10: warning: variable 'cell_value' set but not used [-Wunused-but-set-variable]
double cell_value;
^
Harshlight.c: In function 'norm':
Harshlight.c:1316:27: warning: unused variable 'sorted2' [-Wunused-variable]
double *sorted; double *sorted2;
^
Harshlight.c: In function 'report_overall_header':
Harshlight.c:1471:3: warning: unknown conversion type character ')' in format [-Wformat=]
PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 215, *diff_br);
^
Harshlight.c:1474:3: warning: unknown conversion type character ')' in format [-Wformat=]
PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 230, *diff_dr);
^
Harshlight.c: In function 'chip_summary':
Harshlight.c:1532:3: warning: unknown conversion type character ')' in format [-Wformat=]
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:1542:3: warning: unknown conversion type character ')' in format [-Wformat=]
PP "%d %d moveto (%.2f%) show\n", x_val_1, y_text - 100, *perc_c);
^
Harshlight.c:1543:3: warning: unknown conversion type character ')' in format [-Wformat=]
PP "%d %d moveto (%.2f%) show\n", x_val_2, y_text - 100, *perc_d);
^
Harshlight.c: In function 'extended_stop':
Harshlight.c:1555:3: warning: unknown conversion type character ')' in format [-Wformat=]
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);
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Harshlight.dll tmp.def Harshlight.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/Harshlight.buildbin-libdir/Harshlight/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Harshlight'
finding HTML links ... done
HarshComp html
HarshExt html
Harshlight html
sim html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'Harshlight' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Harshlight.c -o Harshlight.o
Harshlight.c: In function 'extended_defects':
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: In function 'image_dilation':
Harshlight.c:948:10: warning: variable 'cell_value' set but not used [-Wunused-but-set-variable]
double cell_value;
^
Harshlight.c: In function 'norm':
Harshlight.c:1316:27: warning: unused variable 'sorted2' [-Wunused-variable]
double *sorted; double *sorted2;
^
Harshlight.c: In function 'report_overall_header':
Harshlight.c:1471:3: warning: unknown conversion type character ')' in format [-Wformat=]
PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 215, *diff_br);
^
Harshlight.c:1474:3: warning: unknown conversion type character ')' in format [-Wformat=]
PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 230, *diff_dr);
^
Harshlight.c: In function 'chip_summary':
Harshlight.c:1532:3: warning: unknown conversion type character ')' in format [-Wformat=]
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:1542:3: warning: unknown conversion type character ')' in format [-Wformat=]
PP "%d %d moveto (%.2f%) show\n", x_val_1, y_text - 100, *perc_c);
^
Harshlight.c:1543:3: warning: unknown conversion type character ')' in format [-Wformat=]
PP "%d %d moveto (%.2f%) show\n", x_val_2, y_text - 100, *perc_d);
^
Harshlight.c: In function 'extended_stop':
Harshlight.c:1555:3: warning: unknown conversion type character ')' in format [-Wformat=]
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);
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Harshlight.dll tmp.def Harshlight.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/Harshlight.buildbin-libdir/Harshlight/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Harshlight' as Harshlight_1.54.0.zip
* DONE (Harshlight)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Harshlight' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
Harshlight.Rcheck/examples_i386/Harshlight-Ex.timings
|
Harshlight.Rcheck/examples_x64/Harshlight-Ex.timings
|