Last updated on 2019-12-18 08:54:30 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 4.50 | 38.49 | 42.99 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 4.11 | 29.05 | 33.16 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 79.29 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 75.88 | OK | |||
| r-devel-windows-ix86+x86_64 | 1.0.1 | 16.00 | 97.00 | 113.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.1 | 8.00 | 80.00 | 88.00 | OK | |
| r-patched-linux-x86_64 | 1.0.1 | ERROR | ||||
| r-patched-solaris-x86 | 1.0.1 | 93.80 | OK | |||
| r-release-linux-x86_64 | 1.0.1 | 4.28 | 34.82 | 39.10 | ERROR | |
| r-release-windows-ix86+x86_64 | 1.0.1 | 21.00 | 65.00 | 86.00 | OK | |
| r-release-osx-x86_64 | 1.0.1 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.1 | 7.00 | 96.00 | 103.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.1 | OK |
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in 'abemus-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_scaling_factor
> ### Title: Apply the scaling factor R to get the most suitable
> ### locus-specific AF threshold.
> ### Aliases: apply_scaling_factor
>
> ### ** Examples
>
> sample.info.file <- system.file("extdata", "test_sif_toy.tsv", package = "abemus")
> outdir <- tempdir()
> targetbed <- system.file("extdata", "regions_toy.bed", package = "abemus")
> pacbamfolder_bychrom <- system.file("extdata", "pacbam_data_bychrom", package = "abemus")
> pbem_dir <- system.file("extdata", "BaseErrorModel", package = "abemus")
> controls_dir <- system.file("extdata", "Controls", package = "abemus")
> m<-callsnvs(sample.info.file,outdir,targetbed,pbem_dir,controls_dir,pacbamfolder_bychrom,replicas=1)
[ 2019-12-17 21:10:58 ] Reading the sample.info.file
[ 2019-12-17 21:10:58 ] Reading chromosomes from 'targetbed'
[ 2019-12-17 21:10:58 ] Detection of somatic SNVs in case samples
[ 2019-12-17 21:10:58 ] looking for /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/abemus/extdata/Controls/datathreshold.RData [ ok ]
[ 2019-12-17 21:10:58 ] looking for data.table with AFs > 0 and coverages: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/abemus/extdata/BaseErrorModel/afgtz.tsv [ ok ]
[ 2019-12-17 21:10:58 ] looking for data.table with AFs = 0 and coverages: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/abemus/extdata/BaseErrorModel/afz.RData [ ok ]
[ 2019-12-17 21:10:58 ] evaluating bin: (1.9e+03,1.95e+03]
[ 2019-12-17 21:10:59 ] evaluating bin: (1.55e+03,1.6e+03]
[ 2019-12-17 21:10:59 ] evaluating bin: (2.9e+03,2.95e+03]
[ 2019-12-17 21:10:59 ] evaluating bin: (2.35e+03,2.4e+03]
[ 2019-12-17 21:10:59 ] evaluating bin: (2.4e+03,2.45e+03]
[ 2019-12-17 21:10:59 ] evaluating bin: (3.65e+03,3.7e+03]
[ 2019-12-17 21:10:59 ] evaluating bin: (750,800]
[ 2019-12-17 21:11:00 ] evaluating bin: (1.4e+03,1.45e+03]
[ 2019-12-17 21:11:00 ] evaluating bin: (1.45e+03,1.5e+03]
[ 2019-12-17 21:11:00 ] evaluating bin: (2.65e+03,2.7e+03]
[ 2019-12-17 21:11:00 ] evaluating bin: (1.2e+03,1.25e+03]
[ 2019-12-17 21:11:00 ] evaluating bin: (3.05e+03,3.1e+03]
[ 2019-12-17 21:11:00 ] evaluating bin: (4.15e+03,4.2e+03]
[ 2019-12-17 21:11:00 ] evaluating bin: (950,1e+03]
[ 2019-12-17 21:11:01 ] evaluating bin: (1.3e+03,1.35e+03]
[ 2019-12-17 21:11:01 ] evaluating bin: (2.15e+03,2.2e+03]
[ 2019-12-17 21:11:01 ] evaluating bin: (2.85e+03,2.9e+03]
[ 2019-12-17 21:11:01 ] evaluating bin: (3.25e+03,3.3e+03]
[ 2019-12-17 21:11:01 ] evaluating bin: (800,850]
[ 2019-12-17 21:11:01 ] evaluating bin: (1.05e+03,1.1e+03]
[ 2019-12-17 21:11:01 ] evaluating bin: (1.65e+03,1.7e+03]
[ 2019-12-17 21:11:01 ] evaluating bin: (1.75e+03,1.8e+03]
[ 2019-12-17 21:11:02 ] evaluating bin: (1.8e+03,1.85e+03]
[ 2019-12-17 21:11:02 ] evaluating bin: (2.8e+03,2.85e+03]
[ 2019-12-17 21:11:02 ] evaluating bin: (3.35e+03,3.4e+03]
[ 2019-12-17 21:11:02 ] evaluating bin: (4.35e+03,4.4e+03]
[ 2019-12-17 21:11:02 ] evaluating bin: (450,500]
[ 2019-12-17 21:11:02 ] evaluating bin: (1.25e+03,1.3e+03]
[ 2019-12-17 21:11:02 ] evaluating bin: (1.5e+03,1.55e+03]
[ 2019-12-17 21:11:02 ] evaluating bin: (1.85e+03,1.9e+03]
[ 2019-12-17 21:11:02 ] evaluating bin: (2.7e+03,2.75e+03]
[ 2019-12-17 21:11:03 ] evaluating bin: (3.15e+03,3.2e+03]
[ 2019-12-17 21:11:03 ] evaluating bin: (3.85e+03,3.9e+03]
[ 2019-12-17 21:11:03 ] evaluating bin: (500,550]
[ 2019-12-17 21:11:03 ] evaluating bin: (600,650]
[ 2019-12-17 21:11:03 ] evaluating bin: (700,750]
[ 2019-12-17 21:11:03 ] evaluating bin: (2.05e+03,2.1e+03]
[ 2019-12-17 21:11:03 ] evaluating bin: (2.2e+03,2.25e+03]
[ 2019-12-17 21:11:03 ] evaluating bin: (2.95e+03,3e+03]
[ 2019-12-17 21:11:03 ] evaluating bin: (3.3e+03,3.35e+03]
[ 2019-12-17 21:11:03 ] evaluating bin: (1e+03,1.05e+03]
[ 2019-12-17 21:11:03 ] evaluating bin: (1.1e+03,1.15e+03]
[ 2019-12-17 21:11:03 ] evaluating bin: (1.6e+03,1.65e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (1.7e+03,1.75e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (1.95e+03,2e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (2e+03,2.05e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (2.5e+03,2.55e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (2.6e+03,2.65e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (3e+03,3.05e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (3.4e+03,3.45e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (3.8e+03,3.85e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (100,150]
[ 2019-12-17 21:11:04 ] evaluating bin: (150,200]
[ 2019-12-17 21:11:04 ] evaluating bin: (300,350]
[ 2019-12-17 21:11:04 ] evaluating bin: (400,450]
[ 2019-12-17 21:11:04 ] evaluating bin: (550,600]
[ 2019-12-17 21:11:04 ] evaluating bin: (650,700]
[ 2019-12-17 21:11:04 ] evaluating bin: (850,900]
[ 2019-12-17 21:11:04 ] evaluating bin: (900,950]
[ 2019-12-17 21:11:04 ] evaluating bin: (1.15e+03,1.2e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (1.35e+03,1.4e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (2.1e+03,2.15e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (3.2e+03,3.25e+03]
[ 2019-12-17 21:11:04 ] evaluating bin: (3.95e+03,4e+03]
Warning in gzfile(file, "wb") :
cannot open compressed file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/abemus/extdata/Controls/tab1r_0.995_b.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: callsnvs -> adjust_af_threshold_table -> save -> gzfile
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘abemus-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_scaling_factor
> ### Title: Apply the scaling factor R to get the most suitable
> ### locus-specific AF threshold.
> ### Aliases: apply_scaling_factor
>
> ### ** Examples
>
> sample.info.file <- system.file("extdata", "test_sif_toy.tsv", package = "abemus")
> outdir <- tempdir()
> targetbed <- system.file("extdata", "regions_toy.bed", package = "abemus")
> pacbamfolder_bychrom <- system.file("extdata", "pacbam_data_bychrom", package = "abemus")
> pbem_dir <- system.file("extdata", "BaseErrorModel", package = "abemus")
> controls_dir <- system.file("extdata", "Controls", package = "abemus")
> m<-callsnvs(sample.info.file,outdir,targetbed,pbem_dir,controls_dir,pacbamfolder_bychrom,replicas=1)
[ 2019-12-17 19:15:39 ] Reading the sample.info.file
[ 2019-12-17 19:15:39 ] Reading chromosomes from 'targetbed'
[ 2019-12-17 19:15:39 ] Detection of somatic SNVs in case samples
[ 2019-12-17 19:15:39 ] looking for /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/abemus/extdata/Controls/datathreshold.RData [ ok ]
[ 2019-12-17 19:15:39 ] looking for data.table with AFs > 0 and coverages: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/abemus/extdata/BaseErrorModel/afgtz.tsv [ ok ]
[ 2019-12-17 19:15:39 ] looking for data.table with AFs = 0 and coverages: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/abemus/extdata/BaseErrorModel/afz.RData [ ok ]
[ 2019-12-17 19:15:39 ] evaluating bin: (1.9e+03,1.95e+03]
[ 2019-12-17 19:15:40 ] evaluating bin: (1.55e+03,1.6e+03]
[ 2019-12-17 19:15:40 ] evaluating bin: (2.9e+03,2.95e+03]
[ 2019-12-17 19:15:40 ] evaluating bin: (2.35e+03,2.4e+03]
[ 2019-12-17 19:15:40 ] evaluating bin: (2.4e+03,2.45e+03]
[ 2019-12-17 19:15:40 ] evaluating bin: (3.65e+03,3.7e+03]
[ 2019-12-17 19:15:40 ] evaluating bin: (750,800]
[ 2019-12-17 19:15:40 ] evaluating bin: (1.4e+03,1.45e+03]
[ 2019-12-17 19:15:40 ] evaluating bin: (1.45e+03,1.5e+03]
[ 2019-12-17 19:15:41 ] evaluating bin: (2.65e+03,2.7e+03]
[ 2019-12-17 19:15:41 ] evaluating bin: (1.2e+03,1.25e+03]
[ 2019-12-17 19:15:41 ] evaluating bin: (3.05e+03,3.1e+03]
[ 2019-12-17 19:15:41 ] evaluating bin: (4.15e+03,4.2e+03]
[ 2019-12-17 19:15:41 ] evaluating bin: (950,1e+03]
[ 2019-12-17 19:15:42 ] evaluating bin: (1.3e+03,1.35e+03]
[ 2019-12-17 19:15:42 ] evaluating bin: (2.15e+03,2.2e+03]
[ 2019-12-17 19:15:42 ] evaluating bin: (2.85e+03,2.9e+03]
[ 2019-12-17 19:15:42 ] evaluating bin: (3.25e+03,3.3e+03]
[ 2019-12-17 19:15:42 ] evaluating bin: (800,850]
[ 2019-12-17 19:15:42 ] evaluating bin: (1.05e+03,1.1e+03]
[ 2019-12-17 19:15:42 ] evaluating bin: (1.65e+03,1.7e+03]
[ 2019-12-17 19:15:42 ] evaluating bin: (1.75e+03,1.8e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (1.8e+03,1.85e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (2.8e+03,2.85e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (3.35e+03,3.4e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (4.35e+03,4.4e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (450,500]
[ 2019-12-17 19:15:43 ] evaluating bin: (1.25e+03,1.3e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (1.5e+03,1.55e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (1.85e+03,1.9e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (2.7e+03,2.75e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (3.15e+03,3.2e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (3.85e+03,3.9e+03]
[ 2019-12-17 19:15:43 ] evaluating bin: (500,550]
[ 2019-12-17 19:15:44 ] evaluating bin: (600,650]
[ 2019-12-17 19:15:44 ] evaluating bin: (700,750]
[ 2019-12-17 19:15:44 ] evaluating bin: (2.05e+03,2.1e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (2.2e+03,2.25e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (2.95e+03,3e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (3.3e+03,3.35e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (1e+03,1.05e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (1.1e+03,1.15e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (1.6e+03,1.65e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (1.7e+03,1.75e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (1.95e+03,2e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (2e+03,2.05e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (2.5e+03,2.55e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (2.6e+03,2.65e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (3e+03,3.05e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (3.4e+03,3.45e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (3.8e+03,3.85e+03]
[ 2019-12-17 19:15:44 ] evaluating bin: (100,150]
[ 2019-12-17 19:15:44 ] evaluating bin: (150,200]
[ 2019-12-17 19:15:44 ] evaluating bin: (300,350]
[ 2019-12-17 19:15:44 ] evaluating bin: (400,450]
[ 2019-12-17 19:15:44 ] evaluating bin: (550,600]
[ 2019-12-17 19:15:44 ] evaluating bin: (650,700]
[ 2019-12-17 19:15:44 ] evaluating bin: (850,900]
[ 2019-12-17 19:15:45 ] evaluating bin: (900,950]
[ 2019-12-17 19:15:45 ] evaluating bin: (1.15e+03,1.2e+03]
[ 2019-12-17 19:15:45 ] evaluating bin: (1.35e+03,1.4e+03]
[ 2019-12-17 19:15:45 ] evaluating bin: (2.1e+03,2.15e+03]
[ 2019-12-17 19:15:45 ] evaluating bin: (3.2e+03,3.25e+03]
[ 2019-12-17 19:15:45 ] evaluating bin: (3.95e+03,4e+03]
Warning in gzfile(file, "wb") :
cannot open compressed file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/abemus/extdata/Controls/tab1r_0.995_b.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: callsnvs -> adjust_af_threshold_table -> save -> gzfile
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘abemus-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_scaling_factor
> ### Title: Apply the scaling factor R to get the most suitable
> ### locus-specific AF threshold.
> ### Aliases: apply_scaling_factor
>
> ### ** Examples
>
> sample.info.file <- system.file("extdata", "test_sif_toy.tsv", package = "abemus")
> outdir <- tempdir()
> targetbed <- system.file("extdata", "regions_toy.bed", package = "abemus")
> pacbamfolder_bychrom <- system.file("extdata", "pacbam_data_bychrom", package = "abemus")
> pbem_dir <- system.file("extdata", "BaseErrorModel", package = "abemus")
> controls_dir <- system.file("extdata", "Controls", package = "abemus")
> m<-callsnvs(sample.info.file,outdir,targetbed,pbem_dir,controls_dir,pacbamfolder_bychrom,replicas=1)
[ 2019-12-16 12:19:08 ] Reading the sample.info.file
[ 2019-12-16 12:19:08 ] Reading chromosomes from 'targetbed'
[ 2019-12-16 12:19:08 ] Detection of somatic SNVs in case samples
[ 2019-12-16 12:19:08 ] looking for /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/abemus/extdata/Controls/datathreshold.RData [ ok ]
[ 2019-12-16 12:19:08 ] looking for data.table with AFs > 0 and coverages: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/abemus/extdata/BaseErrorModel/afgtz.tsv [ ok ]
[ 2019-12-16 12:19:08 ] looking for data.table with AFs = 0 and coverages: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/abemus/extdata/BaseErrorModel/afz.RData [ ok ]
[ 2019-12-16 12:19:08 ] evaluating bin: (1.9e+03,1.95e+03]
[ 2019-12-16 12:19:09 ] evaluating bin: (1.55e+03,1.6e+03]
[ 2019-12-16 12:19:09 ] evaluating bin: (2.9e+03,2.95e+03]
[ 2019-12-16 12:19:09 ] evaluating bin: (2.35e+03,2.4e+03]
[ 2019-12-16 12:19:09 ] evaluating bin: (2.4e+03,2.45e+03]
[ 2019-12-16 12:19:09 ] evaluating bin: (3.65e+03,3.7e+03]
[ 2019-12-16 12:19:09 ] evaluating bin: (750,800]
[ 2019-12-16 12:19:10 ] evaluating bin: (1.4e+03,1.45e+03]
[ 2019-12-16 12:19:10 ] evaluating bin: (1.45e+03,1.5e+03]
[ 2019-12-16 12:19:10 ] evaluating bin: (2.65e+03,2.7e+03]
[ 2019-12-16 12:19:10 ] evaluating bin: (1.2e+03,1.25e+03]
[ 2019-12-16 12:19:10 ] evaluating bin: (3.05e+03,3.1e+03]
[ 2019-12-16 12:19:10 ] evaluating bin: (4.15e+03,4.2e+03]
[ 2019-12-16 12:19:10 ] evaluating bin: (950,1e+03]
[ 2019-12-16 12:19:10 ] evaluating bin: (1.3e+03,1.35e+03]
[ 2019-12-16 12:19:10 ] evaluating bin: (2.15e+03,2.2e+03]
[ 2019-12-16 12:19:11 ] evaluating bin: (2.85e+03,2.9e+03]
[ 2019-12-16 12:19:11 ] evaluating bin: (3.25e+03,3.3e+03]
[ 2019-12-16 12:19:11 ] evaluating bin: (800,850]
[ 2019-12-16 12:19:11 ] evaluating bin: (1.05e+03,1.1e+03]
[ 2019-12-16 12:19:11 ] evaluating bin: (1.65e+03,1.7e+03]
[ 2019-12-16 12:19:11 ] evaluating bin: (1.75e+03,1.8e+03]
[ 2019-12-16 12:19:11 ] evaluating bin: (1.8e+03,1.85e+03]
[ 2019-12-16 12:19:11 ] evaluating bin: (2.8e+03,2.85e+03]
[ 2019-12-16 12:19:12 ] evaluating bin: (3.35e+03,3.4e+03]
[ 2019-12-16 12:19:12 ] evaluating bin: (4.35e+03,4.4e+03]
[ 2019-12-16 12:19:12 ] evaluating bin: (450,500]
[ 2019-12-16 12:19:12 ] evaluating bin: (1.25e+03,1.3e+03]
[ 2019-12-16 12:19:12 ] evaluating bin: (1.5e+03,1.55e+03]
[ 2019-12-16 12:19:12 ] evaluating bin: (1.85e+03,1.9e+03]
[ 2019-12-16 12:19:12 ] evaluating bin: (2.7e+03,2.75e+03]
[ 2019-12-16 12:19:12 ] evaluating bin: (3.15e+03,3.2e+03]
[ 2019-12-16 12:19:12 ] evaluating bin: (3.85e+03,3.9e+03]
[ 2019-12-16 12:19:12 ] evaluating bin: (500,550]
[ 2019-12-16 12:19:12 ] evaluating bin: (600,650]
[ 2019-12-16 12:19:12 ] evaluating bin: (700,750]
[ 2019-12-16 12:19:13 ] evaluating bin: (2.05e+03,2.1e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (2.2e+03,2.25e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (2.95e+03,3e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (3.3e+03,3.35e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (1e+03,1.05e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (1.1e+03,1.15e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (1.6e+03,1.65e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (1.7e+03,1.75e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (1.95e+03,2e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (2e+03,2.05e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (2.5e+03,2.55e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (2.6e+03,2.65e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (3e+03,3.05e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (3.4e+03,3.45e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (3.8e+03,3.85e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (100,150]
[ 2019-12-16 12:19:13 ] evaluating bin: (150,200]
[ 2019-12-16 12:19:13 ] evaluating bin: (300,350]
[ 2019-12-16 12:19:13 ] evaluating bin: (400,450]
[ 2019-12-16 12:19:13 ] evaluating bin: (550,600]
[ 2019-12-16 12:19:13 ] evaluating bin: (650,700]
[ 2019-12-16 12:19:13 ] evaluating bin: (850,900]
[ 2019-12-16 12:19:13 ] evaluating bin: (900,950]
[ 2019-12-16 12:19:13 ] evaluating bin: (1.15e+03,1.2e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (1.35e+03,1.4e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (2.1e+03,2.15e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (3.2e+03,3.25e+03]
[ 2019-12-16 12:19:13 ] evaluating bin: (3.95e+03,4e+03]
Warning in gzfile(file, "wb") :
cannot open compressed file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/abemus/extdata/Controls/tab1r_0.995_b.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: callsnvs -> adjust_af_threshold_table -> save -> gzfile
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘abemus-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_scaling_factor
> ### Title: Apply the scaling factor R to get the most suitable
> ### locus-specific AF threshold.
> ### Aliases: apply_scaling_factor
>
> ### ** Examples
>
> sample.info.file <- system.file("extdata", "test_sif_toy.tsv", package = "abemus")
> outdir <- tempdir()
> targetbed <- system.file("extdata", "regions_toy.bed", package = "abemus")
> pacbamfolder_bychrom <- system.file("extdata", "pacbam_data_bychrom", package = "abemus")
> pbem_dir <- system.file("extdata", "BaseErrorModel", package = "abemus")
> controls_dir <- system.file("extdata", "Controls", package = "abemus")
> m<-callsnvs(sample.info.file,outdir,targetbed,pbem_dir,controls_dir,pacbamfolder_bychrom,replicas=1)
[ 2019-12-17 04:19:11 ] Reading the sample.info.file
[ 2019-12-17 04:19:11 ] Reading chromosomes from 'targetbed'
[ 2019-12-17 04:19:11 ] Detection of somatic SNVs in case samples
[ 2019-12-17 04:19:11 ] looking for /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/abemus/extdata/Controls/datathreshold.RData [ ok ]
[ 2019-12-17 04:19:11 ] looking for data.table with AFs > 0 and coverages: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/abemus/extdata/BaseErrorModel/afgtz.tsv [ ok ]
[ 2019-12-17 04:19:11 ] looking for data.table with AFs = 0 and coverages: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/abemus/extdata/BaseErrorModel/afz.RData [ ok ]
[ 2019-12-17 04:19:11 ] evaluating bin: (1.9e+03,1.95e+03]
[ 2019-12-17 04:19:11 ] evaluating bin: (1.55e+03,1.6e+03]
[ 2019-12-17 04:19:11 ] evaluating bin: (2.9e+03,2.95e+03]
[ 2019-12-17 04:19:11 ] evaluating bin: (2.35e+03,2.4e+03]
[ 2019-12-17 04:19:12 ] evaluating bin: (2.4e+03,2.45e+03]
[ 2019-12-17 04:19:12 ] evaluating bin: (3.65e+03,3.7e+03]
[ 2019-12-17 04:19:12 ] evaluating bin: (750,800]
[ 2019-12-17 04:19:12 ] evaluating bin: (1.4e+03,1.45e+03]
[ 2019-12-17 04:19:12 ] evaluating bin: (1.45e+03,1.5e+03]
[ 2019-12-17 04:19:12 ] evaluating bin: (2.65e+03,2.7e+03]
[ 2019-12-17 04:19:12 ] evaluating bin: (1.2e+03,1.25e+03]
[ 2019-12-17 04:19:12 ] evaluating bin: (3.05e+03,3.1e+03]
[ 2019-12-17 04:19:12 ] evaluating bin: (4.15e+03,4.2e+03]
[ 2019-12-17 04:19:13 ] evaluating bin: (950,1e+03]
[ 2019-12-17 04:19:13 ] evaluating bin: (1.3e+03,1.35e+03]
[ 2019-12-17 04:19:13 ] evaluating bin: (2.15e+03,2.2e+03]
[ 2019-12-17 04:19:13 ] evaluating bin: (2.85e+03,2.9e+03]
[ 2019-12-17 04:19:13 ] evaluating bin: (3.25e+03,3.3e+03]
[ 2019-12-17 04:19:13 ] evaluating bin: (800,850]
[ 2019-12-17 04:19:13 ] evaluating bin: (1.05e+03,1.1e+03]
[ 2019-12-17 04:19:13 ] evaluating bin: (1.65e+03,1.7e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (1.75e+03,1.8e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (1.8e+03,1.85e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (2.8e+03,2.85e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (3.35e+03,3.4e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (4.35e+03,4.4e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (450,500]
[ 2019-12-17 04:19:14 ] evaluating bin: (1.25e+03,1.3e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (1.5e+03,1.55e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (1.85e+03,1.9e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (2.7e+03,2.75e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (3.15e+03,3.2e+03]
[ 2019-12-17 04:19:14 ] evaluating bin: (3.85e+03,3.9e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (500,550]
[ 2019-12-17 04:19:15 ] evaluating bin: (600,650]
[ 2019-12-17 04:19:15 ] evaluating bin: (700,750]
[ 2019-12-17 04:19:15 ] evaluating bin: (2.05e+03,2.1e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (2.2e+03,2.25e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (2.95e+03,3e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (3.3e+03,3.35e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (1e+03,1.05e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (1.1e+03,1.15e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (1.6e+03,1.65e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (1.7e+03,1.75e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (1.95e+03,2e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (2e+03,2.05e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (2.5e+03,2.55e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (2.6e+03,2.65e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (3e+03,3.05e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (3.4e+03,3.45e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (3.8e+03,3.85e+03]
[ 2019-12-17 04:19:15 ] evaluating bin: (100,150]
[ 2019-12-17 04:19:15 ] evaluating bin: (150,200]
[ 2019-12-17 04:19:15 ] evaluating bin: (300,350]
[ 2019-12-17 04:19:16 ] evaluating bin: (400,450]
[ 2019-12-17 04:19:16 ] evaluating bin: (550,600]
[ 2019-12-17 04:19:16 ] evaluating bin: (650,700]
[ 2019-12-17 04:19:16 ] evaluating bin: (850,900]
[ 2019-12-17 04:19:16 ] evaluating bin: (900,950]
[ 2019-12-17 04:19:16 ] evaluating bin: (1.15e+03,1.2e+03]
[ 2019-12-17 04:19:16 ] evaluating bin: (1.35e+03,1.4e+03]
[ 2019-12-17 04:19:16 ] evaluating bin: (2.1e+03,2.15e+03]
[ 2019-12-17 04:19:16 ] evaluating bin: (3.2e+03,3.25e+03]
[ 2019-12-17 04:19:16 ] evaluating bin: (3.95e+03,4e+03]
Warning in gzfile(file, "wb") :
cannot open compressed file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/abemus/extdata/Controls/tab1r_0.995_b.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: callsnvs -> adjust_af_threshold_table -> save -> gzfile
Execution halted
Flavor: r-release-linux-x86_64