Summary  |  Upper directory |  diff  
       Script Time Stamp:    2016-05-15 03:38 UTC (hash: cb9050c) 
       Started:              2024-07-05 18:31 UTC
       Ended:                2024-07-05 21:05 UTC
       Elapsed:                         02:34:40 
Found:                     9  These packages are to be updated
TODO flags:                3  (More to be updated, by TODO)
Up-to-date:                8  OK, Already up-to-date
Not Available:             1  Failed to get update info (indicated as 0.0)
No Master Sites:           0  (usually in files directory)
NotFound (404):            1  MASTER_SITES returns 404, and no recovery
Forbidden(403/550):        1  
Site not in DNS:          48  
Name ends with digit:      0  (The name ends with digits, may give false version)
Matured:                   0  (No update expected)
Texlive:                   0  (Texlive is skipped for now)
META_PACKAGE:              3  (Other than meta-pkgs category)
Confusing:                 3  (Found version wrong, hilighted, only for debug purpose)
Not Listed:                0  
Sum of Above:             77  

Total Checked:            90  
Options used:                 -R -f -m -p /tmp/pkgsrc -c biology -d /home/makoto/public_html/pkgsrc/check-update//.20240705-18 -S biology.html

 *** Above # has so many errors, by so many reasons, don't blame me :-) , thank you.


directoryPackageNow Update-ToTODOMAINTAINERMASTER_SITES (only the first one checked)
biology/R-popbio R-popbio 2.7 ->2.8.pkgsrc-usershttps://cran.r-project.org/src/contrib/
biology/ad2vcf ad2vcf 0.1.6.19 ->0.1.6baconhttps://github.com/auerlab/
biology/azara azara (-1) 2.7 ->0.0mchittur@cs.nhttp://www.ccpn.ac.uk/download/azara/(404)
biology/balance-tui balance-tui 0.1.2 ->0.0pkgsrc-usershttps://static.crates.io/crates/balance-tui/(403)
biology/bcftools bcftools 1.17 ->1.20baconhttps://github.com/samtools/
biology/beagle beagle 5.2 ->0.0pkgsrc-usershttps://faculty.washington.edu/browning/beagle/
biology/biolibc biolibc 0.2.6.4 ->0.2.6baconhttps://github.com/auerlab/
biology/biolibc-tools biolibc-tools 0.1.4.13 ->0.1.4baconhttps://github.com/auerlab/
biology/bioperl bioperl 1.7.7 ->1.0070021.7.8pkgsrc-usershttps://www.cpan.org/modules/by-module/Bio/
biology/bodr bodr (empty) 9 ->0.0jihbed.researhttps://downloads.sourceforge.net/sourceforge/bodr/(DNS)
biology/bwa bwa (DNS) 0.7.17 ->0.7.18baconhttps://github.com/lh3/
biology/coordgenlibs coordgenlibs 1.4.2 ->3.0.22.0.3bsiegerthttps://github.com/schrodinger/
biology/fastp fastp (DNS) 0.22.0 ->0.0baconhttps://github.com/OpenGene/(DNS)
biology/fastq-trim fastq-trim (DNS) 0.1.3 ->0.0baconhttps://github.com/outpaddling/(DNS)
biology/fastqc fastqc (DNS) 0.11.9 ->0.0baconhttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/(DNS)
biology/fastx-toolkit fastx-toolkit (DNS) 0.0.14.6 ->0.0baconhttps://github.com/agordon/(DNS)
biology/filter-fastq filter-fastq (DNS) 0.0.0.20210527 ->0.0pkgsrc-usershttps://github.com/stephenfloor/(DNS)
biology/fluctuate fluctuate (empty) 1.4 ->0.0brook@nmsu.edhttp://evolution.gs.washington.edu/lamarc/fluctuate/(DNS)
biology/gabedit gabedit (DNS) 2.4.8 ->0.0asau@inbox.ruhttps://downloads.sourceforge.net/sourceforge/gabedit/(DNS)
biology/generand generand (DNS) 0.1.2 ->0.0baconhttps://github.com/auerlab/(DNS)
biology/genesplicer genesplicer (DNS) 20030403 ->0.0hdp@cs.nmsu.eftp://ftp.tigr.org/pub/software/GeneSplicer/(DNS)
biology/gffread gffread (DNS) 0.12.7 ->0.0baconhttps://github.com/gpertea/(DNS)
biology/glimmer glimmer (DNS) 2.13 ->0.0hdp@cs.nmsu.eftp://ftp.tigr.org/pub/software/Glimmer/(DNS)
biology/gp gp (DNS) 0.26 ->0.0hdp@cs.nmsu.ehttp://www.bioinformatics.org/genpak/download/(DNS)
biology/gromacs gromacs (DNS) 4.5.5 ->0.02021.1pkgsrc-usersftp://ftp.gromacs.org/pub/gromacs/(DNS)
biology/hisat2 hisat2 (DNS) 2.2.1 ->0.0baconhttps://github.com/DaehwanKimLab/(DNS)
biology/hmmer hmmer (DNS) 3.0 ->0.03.1b2hdp@cs.nmsu.ehttp://eddylab.org/software/hmmer/(DNS)
biology/htslib htslib (DNS) 1.17 ->0.0baconhttps://github.com/samtools/(DNS)
biology/igv igv (DNS) 2.9.2 ->0.0baconhttps://data.broadinstitute.org/igv/projects/downloads/2.9/(DNS)
biology/kallisto kallisto (DNS) 0.50.1 ->0.0baconhttps://github.com/pachterlab/(DNS)
biology/libpll libpll (DNS) 0.3.2 ->0.0thomas.orgis@https://github.com/xflouris/(DNS)
biology/lucy lucy (DNS) 1.20 ->0.0dprice@cs.nmshttps://downloads.sourceforge.net/sourceforge/lucy/(DNS)
biology/maeparser maeparser (DNS) 1.2.4 ->0.0bsiegerthttps://github.com/schrodinger/(DNS)
biology/microsynteny-tools microsynteny-tools (DNS) 0.1.0.175 ->0.0baconhttps://github.com/auerlab/(DNS)
biology/miniasm miniasm (DNS) 0.3 ->0.0pkgsrc-usershttps://github.com/lh3/(DNS)
biology/minimap2 minimap2 (DNS) 2.28 ->0.0pkgsrc-usershttps://github.com/lh3/(DNS)
biology/molsketch molsketch (DNS) 0.8.1 ->0.0pinhttps://downloads.sourceforge.net/sourceforge/molsketch/(DNS)
biology/mopac mopac (DNS) 22.0.6 ->0.0pkgsrc-usershttps://github.com/openmopac/(DNS)
biology/mpqc mpqc (DNS) 2.3.1 ->0.0asau@inbox.ruhttps://downloads.sourceforge.net/sourceforge/mpqc/(DNS)
biology/mummer mummer (DNS) 3.20 ->0.0hdp@cs.nmsu.ehttps://downloads.sourceforge.net/sourceforge/mummer/(DNS)
biology/ncbi-blast+ ncbi-blast+ (DNS) 2.14.1 ->0.0baconhttps://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/(DNS)
biology/openbabel openbabel (DNS) 3.1.1 ->0.0pkgsrc-usershttps://github.com/openbabel/(DNS)
biology/p5-Bio-ASN1-EntrezGene p5-Bio-ASN1-EntrezGene (none) 1.73 ->0.0pkgsrc-usershttps://www.cpan.org/modules/by-module/Bio/(DNS)
biology/pdbalign pdbalign (empty) 20030812 ->0.0hdp@cs.nmsu.eftp://ftp.ebi.ac.uk/pub/software/unix/pdbalign/(DNS)
biology/peak-classifier peak-classifier (DNS) 0.1.4.13 ->0.0baconhttps://github.com/auerlab/(DNS)
biology/primer3 primer3 (DNS) 2.3.6 ->0.0pkgsrc-usershttps://downloads.sourceforge.net/sourceforge/primer3/(DNS)
biology/puzzle puzzle (DNS) 5.2 ->0.0babafou@babafhttp://www.tree-puzzle.de/(DNS)
biology/py-biopython py311-biopython (DNS) 1.81 ->0.0pkgsrc-usershttp://biopython.org/DIST/(DNS)
biology/py-macs2 py311-macs2 (DNS) 2.2.9.1 ->0.0baconhttps://github.com/taoliu/(DNS)
biology/py-macs3 py311-macs3 (DNS) 3.0.1 ->0.0baconhttps://github.com/macs3-project/(DNS)
biology/racon racon (DNS) 1.4.3 ->0.0pkgsrc-usershttps://github.com/isovic/(DNS)
biology/rasmol rasmol (DNS) 2.7.3 ->0.02.7.5.2pkgsrc-usershttp://www.bernstein-plus-sons.com/software/(DNS)
biology/rna-star rna-star (DNS) 2.7.10b ->0.0baconhttps://github.com/alexdobin/(DNS)
biology/samtools samtools (DNS) 1.17 ->0.0baconhttps://github.com/samtools/(DNS)
biology/seqtk seqtk (DNS) 1.4 ->0.0baconhttps://github.com/lh3/(DNS)
biology/sra-tools sra-tools (DNS) 3.0.6 ->0.0baconhttps://github.com/outpaddling/(DNS)
biology/stacks stacks (DNS) 2.60 ->0.0baconhttp://catchenlab.life.illinois.edu/stacks/source/(DNS)
biology/stride stride (empty) 20030804 ->0.0hdp@cs.nmsu.eftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/(DNS)
biology/stringtie stringtie (DNS) 2.1.1 ->0.0baconhttp://ccb.jhu.edu/software/stringtie/dl/(DNS)
biology/trimmomatic Trimmomatic (DNS) 0.38 ->0.0baconhttp://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/(DNS)
biology/vcf-split vcf-split (DNS) 0.1.5.10 ->0.0baconhttps://github.com/auerlab/(DNS)
biology/vcf2hap vcf2hap (DNS) 0.1.6.7 ->0.0baconhttps://github.com/auerlab/(DNS)
biology/vsearch vsearch (DNS) 2.27.1 ->0.0baconhttps://github.com/torognes/(DNS)
biology/xmakemol xmakemol (DNS) 5.16h ->0.0vinsftp://ftp.NetBSD.org/pub/NetBSD/misc/vins/dists/(none)
biology/xylem xylem (DNS) 1.8.7 ->0.0hdp@cs.nmsu.eftp://ftp.cc.umanitoba.ca/psgendb/(none)
biology/nutsqlite nutsqlite (DNS) 2.0.6 ->0.0pkgsrc-usershttps://downloads.sourceforge.net/sourceforge/nut/(DNS)