Last updated on 2025-01-09 01:49:55 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.3.1 | ERROR | ||||
| r-devel-linux-x86_64-debian-gcc | 2.3.1 | 23.11 | 138.81 | 161.92 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.3.1 | 430.51 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.3.1 | 413.66 | OK | |||
| r-devel-windows-x86_64 | 2.3.1 | 43.00 | 227.00 | 270.00 | OK | |
| r-patched-linux-x86_64 | 2.3.1 | 35.17 | 191.45 | 226.62 | OK | |
| r-release-linux-x86_64 | 2.3.1 | 35.53 | 193.64 | 229.17 | OK | |
| r-release-macos-arm64 | 2.3.1 | 67.00 | NOTE | |||
| r-release-macos-x86_64 | 2.3.1 | 151.00 | NOTE | |||
| r-release-windows-x86_64 | 2.3.1 | 44.00 | 226.00 | 270.00 | NOTE | |
| r-oldrel-macos-arm64 | 2.3.1 | 78.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.3.1 | 121.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 2.3.1 | 53.00 | 286.00 | 339.00 | NOTE |
Version: 2.3.1
Check: examples
Result: ERROR
Running examples in ‘sigminer-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: simulation
> ### Title: Simulation Analysis
> ### Aliases: simulation simulate_signature simulate_catalogue
> ### simulate_catalogue_matrix
>
> ### ** Examples
>
> # Generate a catalog
> set.seed(1234)
> catalog <- as.integer(table(sample(1:96, 1000, replace = TRUE)))
> names(catalog) <- paste0("comp", 1:96)
> # Generate a signature
> sig <- catalog / sum(catalog)
>
> # Simulate catalogs
> x1 <- simulate_catalogue(catalog, 10) # 10 mutations
Loading required namespace: matrixStats
Failed with error: ‘there is no package called ‘matrixStats’’
'matrixStats' package is not available, installing it.
Installing package into ‘/home/hornik/tmp/scratch/RtmpsZ7g8y/RLIBS_20f58ac5c71e3’
(as ‘lib’ is unspecified)
* installing *source* package ‘matrixStats’ ...
** package ‘matrixStats’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Debian clang version 19.1.6 (1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6lmibO/R.INSTALL227fdf5f84c977/matrixStats/src'
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c 000.init.c -o 000.init.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c allocMatrix2.c -o allocMatrix2.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c anyMissing.c -o anyMissing.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c binCounts.c -o binCounts.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c binMeans.c -o binMeans.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c colCounts.c -o colCounts.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c colOrderStats.c -o colOrderStats.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c colRanges.c -o colRanges.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c diff2.c -o diff2.o
In file included from diff2.c:10:
In file included from ./diff2_lowlevel.h:15:
./diff2_lowlevel_template.h:75:11: error: call to undeclared function 'Calloc'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
75 | tmp = R_CALLOC(nidxs - lag, X_C_TYPE);
| ^
./000.types.h:64:31: note: expanded from macro 'R_CALLOC'
64 | #define R_CALLOC(num, size) Calloc(num, size)
| ^
In file included from diff2.c:10:
In file included from ./diff2_lowlevel.h:15:
./diff2_lowlevel_template.h:75:33: error: expected expression
75 | tmp = R_CALLOC(nidxs - lag, X_C_TYPE);
| ^
./000.templates-types.h:40:22: note: expanded from macro 'X_C_TYPE'
40 | #define X_C_TYPE int
| ^
In file included from diff2.c:10:
In file included from ./diff2_lowlevel.h:15:
./diff2_lowlevel_template.h:118:5: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
118 | R_FREE(tmp);
| ^
./000.types.h:65:23: note: expanded from macro 'R_FREE'
65 | #define R_FREE(ptr) Free(ptr)
| ^
./diff2_lowlevel_template.h:118:5: note: did you mean 'free'?
./000.types.h:65:23: note: expanded from macro 'R_FREE'
65 | #define R_FREE(ptr) Free(ptr)
| ^
/usr/include/stdlib.h:687:13: note: 'free' declared here
687 | extern void free (void *__ptr) __THROW;
| ^
In file included from diff2.c:10:
In file included from ./diff2_lowlevel.h:19:
./diff2_lowlevel_template.h:75:11: error: call to undeclared function 'Calloc'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
75 | tmp = R_CALLOC(nidxs - lag, X_C_TYPE);
| ^
./000.types.h:64:31: note: expanded from macro 'R_CALLOC'
64 | #define R_CALLOC(num, size) Calloc(num, size)
| ^
In file included from diff2.c:10:
In file included from ./diff2_lowlevel.h:19:
./diff2_lowlevel_template.h:75:33: error: expected expression
75 | tmp = R_CALLOC(nidxs - lag, X_C_TYPE);
| ^
./000.templates-types.h:50:22: note: expanded from macro 'X_C_TYPE'
50 | #define X_C_TYPE double
| ^
In file included from diff2.c:10:
In file included from ./diff2_lowlevel.h:19:
./diff2_lowlevel_template.h:118:5: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
118 | R_FREE(tmp);
| ^
./000.types.h:65:23: note: expanded from macro 'R_FREE'
65 | #define R_FREE(ptr) Free(ptr)
| ^
6 errors generated.
make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:195: diff2.o] Error 1
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6lmibO/R.INSTALL227fdf5f84c977/matrixStats/src'
ERROR: compilation failed for package ‘matrixStats’
* removing ‘/home/hornik/tmp/scratch/RtmpsZ7g8y/RLIBS_20f58ac5c71e3/matrixStats’
Warning in install.packages("matrixStats") :
installation of package ‘matrixStats’ had non-zero exit status
Error in loadNamespace(x) : there is no package called ‘matrixStats’
Calls: simulate_catalogue ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sig_fit_bootstrap_batch 5.116 0.011 6.901
show_cn_group_profile 4.496 0.050 5.686
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.3.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 2.3.1
Check: installed package size
Result: NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
extdata 1.0Mb
help 1.7Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64