Charlotte Soneson
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Rhisat2 |
| Branch: RELEASE_3_9 |
| Last Commit: 1fb99f9 |
| Last Changed Date: 2019-06-11 04:07:47 -0400 (Tue, 11 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:04:07 -0400 (Wed, 16 Oct 2019).
| Package 1374/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rhisat2 1.0.3 Charlotte Soneson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Rhisat2 |
| Version: 1.0.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rhisat2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rhisat2_1.0.3.tar.gz |
| StartedAt: 2019-10-16 06:15:09 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:20:49 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 340.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rhisat2.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rhisat2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rhisat2_1.0.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Rhisat2.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Rhisat2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Rhisat2’ version ‘1.0.3’ * package encoding: UTF-8 * 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 ‘Rhisat2’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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-3.9-bioc/meat/Rhisat2.Rcheck/00check.log’ for details.
Rhisat2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhisat2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘Rhisat2’ ... ** using staged installation ** libs ** arch - /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread mkdir -p ../inst cp hisat2-align-s ../inst/hisat2 cp hisat2-build-s ../inst/hisat2-build /usr/bin/g++ -shared -fPIC -o Rhisat2.so get_info.cpp installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhisat2/00new/Rhisat2/libs ** R ** inst ** 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 (Rhisat2)
Rhisat2.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Rhisat2)
>
> test_check("Rhisat2")
*** Warning ***
'hisat2-build-s' was run directly. It is recommended that you run the wrapper script 'hisat2-build' instead.
[1] "HISAT2 version 2.1.0 by Daehwan Kim ([email protected], http://www.ccb.jhu.edu/people/infphilo)"
[2] "Usage: hisat2-build [options]* "
[3] " reference_in comma-separated list of files with ref sequences"
[4] " hisat2_index_base write ht2 data to files with this dir/basename"
[5] "Options:"
[6] " -c reference sequences given on cmd line (as"
[7] " )"
[8] " -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting"
[9] " -p number of threads"
[10] " --bmax max bucket sz for blockwise suffix-array builder"
[11] " --bmaxdivn max bucket sz as divisor of ref len (default: 4)"
[12] " --dcv diff-cover period for blockwise (default: 1024)"
[13] " --nodc disable diff-cover (algorithm becomes quadratic)"
[14] " -r/--noref don't build .3/.4.ht2 (packed reference) portion"
[15] " -3/--justref just build .3/.4.ht2 (packed reference) portion"
[16] " -o/--offrate SA is sampled every 2^offRate BWT chars (default: 5)"
[17] " -t/--ftabchars # of chars consumed in initial lookup (default: 10)"
[18] " --localoffrate SA (local) is sampled every 2^offRate BWT chars (default: 3)"
[19] " --localftabchars # of chars consumed in initial lookup in a local index (default: 6)"
[20] " --snp SNP file name"
[21] " --haplotype haplotype file name"
[22] " --ss Splice site file name"
[23] " --exon Exon file name"
[24] " --seed seed for random number generator"
[25] " -q/--quiet verbose output (for debugging)"
[26] " -h/--help print detailed description of tool and its options"
[27] " --usage print this usage message"
[28] " --version print version information and quit"
*** Warning ***
'hisat2-align' was run directly. It is recommended that you run the wrapper script 'hisat2' instead.
[1] "HISAT2 version 2.1.0 by Daehwan Kim ([email protected], www.ccb.jhu.edu/people/infphilo)"
[2] "Usage: "
[3] " hisat2-align [options]* -x {-1 -2 | -U } [-S ]"
[4] ""
[5] " Index filename prefix (minus trailing .X.ht2)."
[6] " Files with #1 mates, paired with files in ."
[7] " Files with #2 mates, paired with files in ."
[8] " Files with unpaired reads."
[9] " File for SAM output (default: stdout)"
[10] ""
[11] " , , can be comma-separated lists (no whitespace) and can be"
[12] " specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'."
[13] ""
[14] "Options (defaults in parentheses):"
[15] ""
[16] " Input:"
[17] " -q query input files are FASTQ .fq/.fastq (default)"
[18] " --qseq query input files are in Illumina's qseq format"
[19] " -f query input files are (multi-)FASTA .fa/.mfa"
[20] " -r query input files are raw one-sequence-per-line"
[21] " -c , , are sequences themselves, not files"
[22] " -s/--skip skip the first reads/pairs in the input (none)"
[23] " -u/--upto stop after first reads/pairs (no limit)"
[24] " -5/--trim5 trim bases from 5'/left end of reads (0)"
[25] " -3/--trim3 trim bases from 3'/right end of reads (0)"
[26] " --phred33 qualities are Phred+33 (default)"
[27] " --phred64 qualities are Phred+64"
[28] " --int-quals qualities encoded as space-delimited integers"
[29] ""
[30] " Alignment:"
[31] " --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)"
[32] " --ignore-quals treat all quality values as 30 on Phred scale (off)"
[33] " --nofw do not align forward (original) version of read (off)"
[34] " --norc do not align reverse-complement version of read (off)"
[35] ""
[36] " Spliced Alignment:"
[37] " --pen-cansplice penalty for a canonical splice site (0)"
[38] " --pen-noncansplice penalty for a non-canonical splice site (12)"
[39] " --pen-canintronlen penalty for long introns (G,-8,1) with canonical splice sites"
[40] " --pen-noncanintronlen penalty for long introns (G,-8,1) with noncanonical splice sites"
[41] " --min-intronlen minimum intron length (20)"
[42] " --max-intronlen maximum intron length (500000)"
[43] " --known-splicesite-infile provide a list of known splice sites"
[44] " --novel-splicesite-outfile report a list of splice sites"
[45] " --novel-splicesite-infile provide a list of novel splice sites"
[46] " --no-temp-splicesite disable the use of splice sites found"
[47] " --no-spliced-alignment disable spliced alignment"
[48] " --rna-strandness specify strand-specific information (unstranded)"
[49] " --tmo reports only those alignments within known transcriptome"
[50] " --dta reports alignments tailored for transcript assemblers"
[51] " --dta-cufflinks reports alignments tailored specifically for cufflinks"
[52] " --avoid-pseudogene tries to avoid aligning reads to pseudogenes (experimental option)\023"
[53] " --no-templatelen-adjustment disables template length adjustment for RNA-seq reads"
[54] ""
[55] " Scoring:"
[56] " --mp , max and min penalties for mismatch; lower qual = lower penalty <6,2>"
[57] " --sp , max and min penalties for soft-clipping; lower qual = lower penalty <2,1>"
[58] " --no-softclip no soft-clipping"
[59] " --np penalty for non-A/C/G/Ts in read/ref (1)"
[60] " --rdg , read gap open, extend penalties (5,3)"
[61] " --rfg , reference gap open, extend penalties (5,3)"
[62] " --score-min min acceptable alignment score w/r/t read length"
[63] " (L,0.0,-0.2)"
[64] ""
[65] " Reporting:"
[66] " -k (default: 5) report up to alns per read"
[67] ""
[68] " Paired-end:"
[69] " -I/--minins minimum fragment length (0), only valid with --no-spliced-alignment"
[70] " -X/--maxins maximum fragment length (500), only valid with --no-spliced-alignment"
[71] " --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)"
[72] " --no-mixed suppress unpaired alignments for paired reads"
[73] " --no-discordant suppress discordant alignments for paired reads"
[74] ""
[75] " Output:"
[76] " -t/--time print wall-clock time taken by search phases"
[77] " --summary-file print alignment summary to this file."
[78] " --new-summary print alignment summary in a new style, which is more machine-friendly."
[79] " --quiet print nothing to stderr except serious errors"
[80] " --met-file send metrics to file at (off)"
[81] " --met-stderr send metrics to stderr (off)"
[82] " --met report internal counters & metrics every secs (1)"
[83] " --no-head supppress header lines, i.e. lines starting with @"
[84] " --no-sq supppress @SQ header lines"
[85] " --rg-id set read group id, reflected in @RG line and RG:Z: opt field"
[86] " --rg add (\"lab:value\") to @RG line of SAM header."
[87] " Note: @RG line only printed when --rg-id is set."
[88] " --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments."
[89] ""
[90] " Performance:"
[91] " -o/--offrate override offrate of index; must be >= index's offrate"
[92] " -p/--threads number of alignment threads to launch (1)"
[93] " --reorder force SAM output order to match order of input reads"
[94] " --mm use memory-mapped I/O for index; many 'hisat2's can share"
[95] ""
[96] " Other:"
[97] " --qc-filter filter out reads that are bad according to QSEQ filter"
[98] " --seed seed for random number generator (0)"
[99] " --non-deterministic seed rand. gen. arbitrarily instead of using read attributes"
[100] " --remove-chrname remove 'chr' from reference names in alignment"
[101] " --add-chrname add 'chr' to reference names in alignment "
[102] " --version print version information and quit"
[103] " -h/--help print this usage message"
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhisat2/hisat2 version 2.1.0"
[2] "64-bit"
[3] "Built on celaya2.bioconductor.org"
[4] "Tue Oct 15 19:22:51 EDT 2019"
[5] "Compiler: InstalledDir: /Library/Developer/CommandLineTools/usr/bin"
[6] "Options: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY"
[7] "Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}"
Settings:
Output files: "/tmp/RtmpVUfUyu/hisat2indexdir/index.*.ht2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhisat2/extdata/refs/chr1.fa
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 18650 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 18650 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 26955
fchr[G]: 49554
fchr[T]: 72459
fchr[$]: 99465
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4227718 bytes to primary GFM file: /tmp/RtmpVUfUyu/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: /tmp/RtmpVUfUyu/hisat2indexdir/index.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 45363 bytes to primary GFM file: /tmp/RtmpVUfUyu/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: /tmp/RtmpVUfUyu/hisat2indexdir/index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HierEbwt constructor
Headers:
len: 99465
gbwtLen: 99466
nodes: 99466
sz: 24867
gbwtSz: 24867
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 0
eftabSz: 0
ftabLen: 1048577
ftabSz: 4194308
offsLen: 6217
offsSz: 24868
lineSz: 64
sideSz: 64
sideGbwtSz: 48
sideGbwtLen: 192
numSides: 519
numLines: 519
gbwtTotLen: 33216
gbwtTotSz: 33216
reverse: 0
linearFM: Yes
Total time for call to driver() for forward index: 00:00:01
Settings:
Output files: "/tmp/RtmpVUfUyu/hisat2indexdir/index.*.ht2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhisat2/extdata/refs/chr1.fa
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 18650 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 18650 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 26955
fchr[G]: 49554
fchr[T]: 72459
fchr[$]: 99465
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4227718 bytes to primary GFM file: /tmp/RtmpVUfUyu/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: /tmp/RtmpVUfUyu/hisat2indexdir/index.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 45363 bytes to primary GFM file: /tmp/RtmpVUfUyu/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: /tmp/RtmpVUfUyu/hisat2indexdir/index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HierEbwt constructor
Headers:
len: 99465
gbwtLen: 99466
nodes: 99466
sz: 24867
gbwtSz: 24867
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 0
eftabSz: 0
ftabLen: 1048577
ftabSz: 4194308
offsLen: 6217
offsSz: 24868
lineSz: 64
sideSz: 64
sideGbwtSz: 48
sideGbwtLen: 192
numSides: 519
numLines: 519
gbwtTotLen: 33216
gbwtTotSz: 33216
reverse: 0
linearFM: Yes
Total time for call to driver() for forward index: 00:00:00
4 reads; of these:
4 (100.00%) were unpaired; of these:
2 (50.00%) aligned 0 times
2 (50.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
50.00% overall alignment rate
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 32 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
27.139 1.883 29.000
Rhisat2.Rcheck/Rhisat2-Ex.timings
| name | user | system | elapsed | |
| extract_splice_sites | 3.508 | 0.315 | 3.830 | |
| hisat2 | 0.287 | 0.106 | 0.407 | |
| hisat2_build | 0.274 | 0.086 | 0.362 | |
| hisat2_build_usage | 0.010 | 0.011 | 0.024 | |
| hisat2_usage | 0.018 | 0.014 | 0.035 | |
| hisat2_version | 0.008 | 0.008 | 0.019 | |