biology/fasta3 was marked as BROKEN due to a checksum mismatch. It is now scheduled for removal on August 20. I am now fixing the build problems and asking for maintainership of the port. Johann (the current maintainer) has not been very active lately and he already has agreed on me taking maintainership of other biology/ ports (p5-bioperl, emboss (which BTW I still have to finish)). Although there are new versions of fasta3 (see ftp://ftp.virginia.edu/pub/fasta/), in this PR I am just fixing the problems with fasta33t08d4. I don't know what could have changed in the files, since the version has remained the same ... so the answer about the change in checksum is: I really don't know what caused the checksum mismatch. I've checked the pkg-plist and nothing new is installed ... so to fix it I just went to ftp://ftp.virginia.edu/pub/fasta/, downloaded fasta33t08d4.shar.Z and updated the distinfo file accordingly. Now everything builds and installs fine. I hope this is enough to save the port. I am planning to update it soon to the latest version (fasta34t24b1). But that will be in another PR :)
Responsible Changed From-To: freebsd-ports-bugs->wjv Over to the current maintainer.
State Changed From-To: open->feedback Do you agree to pass maintainership to the submitter?
Unfortunately, when a checksum changes without a revision bump, we ask maintainers (and prospective maintainers :-) ) to download both the old and the new tarballs and themselves verify that nothing untoward has happened (e.g. the introduction of trojan horses). This is to keep the Ports Collection as safe as possible. To do this, you'll need to fetch the old copy from one of the FreeBSD mastersites and unpack it and do a diff -ruN with the new one, and then document what changed between the two.
+----[ Mark Linimon <linimon@lonesome.com> (30.Jun.2004 03:34): | | Unfortunately, when a checksum changes without a revision bump, we | ask maintainers (and prospective maintainers :-) ) to download both | the old and the new tarballs and themselves verify that nothing | untoward has happened (e.g. the introduction of trojan horses). This | is to keep the Ports Collection as safe as possible. | | To do this, you'll need to fetch the old copy from one of the | FreeBSD mastersites and unpack it and do a diff -ruN with the | new one, and then document what changed between the two. | +----] Indeed! I've downloaded the sources referenced by the current state of the biology/fasta3 port: MD5 (fasta33t08d4.shar.Z) = 66f0c4731a6ff1cf123067c6ec46e352 SIZE (fasta33t08d4.shar.Z) = 690366 ftp://ftp.freebsd.org/pub/FreeBSD/ports/distfiles/fasta33t08d4.shar.Z and compared it to the sources as they are provided by the author: MD5 (fasta33t08d4.shar.Z) = e6217268e122b2ca7c51b443425e40e3 SIZE (fasta33t08d4.shar.Z) = 685912 ftp://ftp.virginia.edu/pub/fasta/fasta33t08d4.shar.Z and this is the output of diff -ruN, which looks pretty inofensive to me: diff -ruN old/Makefile.linux new/Makefile.linux --- old/Makefile.linux Wed Jun 30 10:37:28 2004 +++ new/Makefile.linux Wed Jun 30 10:38:10 2004 @@ -13,7 +13,7 @@ # # for DEC/Compaq Alpha/LINUX, use gcc -mieee -g to avoid buggy compilers -CC= gcc -g -O +CC= gcc -O # this file works for x86 LINUX diff -ruN old/test.log new/test.log --- old/test.log Wed Jun 30 10:37:31 2004 +++ new/test.log Wed Dec 31 21:00:00 1969 @@ -1,182 +0,0 @@ - -starting fasta33_t - protein Sat Apr 7 11:05:00 EDT 2001 on wrpx1.bioch.Virginia.EDU -Linux wrpx1.bioch.Virginia.EDU 2.2.14 #1 SMP Wed Feb 16 13:22:13 EST 2000 i686 unknown - - FASTA searches a protein or DNA sequence data bank - version 3.3t08d4 Mar. 27, 2001 -Please cite: - W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 - -mgstm1.aa:100-218: 119 aa - >GT8.7 | 40001 90043 | transl. of pa875.con, 19 to 675 - vs NCBI/Blast Swissprot library -searching /slib2/blast/swissprot.lseg library - - opt E() -< 20 606 0:==== - 22 3 0:= one = represents 193 library sequences - 24 5 0:= - 26 10 2:* - 28 17 21:* - 30 40 130:* - 32 140 502:= * - 34 417 1361:=== * - 36 1379 2796:======== * - 38 3830 4621:==================== * - 40 6869 6446:=================================*== - 42 10274 7879:========================================*============= - 44 11545 8691:=============================================*============== - 46 9907 8852:=============================================*====== - 48 8245 8475:===========================================* - 50 6813 7733:==================================== * - 52 5431 6799:============================= * - 54 4561 5807:======================== * - 56 4038 4851:===================== * - 58 3499 3983:=================== * - 60 3098 3226:================* - 62 2513 2586:=============* - 64 2191 2057:==========*= - 66 1870 1626:========*= - 68 1441 1279:======*= - 70 1205 1002:=====*= - 72 1031 783:====*= - 74 791 611:===*= - 76 698 475:==*= - 78 523 369:=*= - 80 408 287:=*= - 82 317 219:=* - 84 250 174:*= - 86 211 134:*= - 88 142 104:* inset = represents 2 library sequences - 90 115 81:* - 92 81 62:* :==============================*========= - 94 58 48:* :=======================*===== - 96 39 37:* :==================*= - 98 30 29:* :==============* - 100 21 22:* :==========* - 102 21 17:* :========*== - 104 15 13:* :======*= - 106 14 10:* :====*== - 108 6 8:* :===* - 110 4 6:* :==* - 112 7 5:* :==*= - 114 3 4:* :=* - 116 3 3:* :=* - 118 0 2:* :* ->120 10 2:* :*==== -34569641 residues in 94745 sequences - statistics extrapolated from 60000 to 94238 sequences - (shuffled) Expectation_n fit: rho(ln(x))= 5.2860+/-0.000165; mu= -3.5082+/- 0.009 - mean_var=77.6729+/-15.828, 0's: 499 Z-trim: 0 B-trim: 0 in 0/63 - Lambda= 0.1455 - Kolmogorov-Smirnov statistic: 0.0382 (N=29) at 38 - -FASTA (3.36 June 2000) function [optimized, PAM250 matrix (17:-8)xS] ktup: 2 - join: 36, opt: 24, gap-pen: -12/ -2, width: 16 - Scan time: 1.010 -The best scores are: opt bits E(94238) -gi|121716|sp|P10649|GTM1_MOUSE GLUTATHIONE S-TRA ( 218) 658 148 5.2e-36 -gi|121717|sp|P04905|GTM1_RAT GLUTATHIONE S-TRANS ( 218) 635 144 1.5e-34 -gi|399829|sp|Q00285|GTMU_CRILO GLUTATHIONE S-TRA ( 218) 604 137 1.3e-32 -gi|121720|sp|P19639|GTM3_MOUSE GLUTATHIONE S-TRA ( 218) 600 136 2.4e-32 -gi|121718|sp|P15626|GTM2_MOUSE GLUTATHIONE S-TRA ( 218) 566 129 3.4e-30 -gi|121719|sp|P08010|GTM2_RAT GLUTATHIONE S-TRANS ( 218) 564 129 4.5e-30 -gi|121722|sp|P16413|GTMU_CAVPO GLUTATHIONE S-TRA ( 217) 562 128 6e-30 -gi|232206|sp|P30116|GTMU_MESAU GLUTATHIONE S-TRA ( 218) 560 128 8.1e-30 -gi|232204|sp|P28161|GTM2_HUMAN GLUTATHIONE S-TRA ( 218) 529 121 7.4e-28 -gi|121721|sp|P08009|GTM3_RAT GLUTATHIONE S-TRANS ( 218) 521 120 2.4e-27 -gi|1170098|sp|P46409|GTMU_RABIT GLUTATHIONE S-TR ( 218) 500 115 5e-26 -gi|1346207|sp|P48774|GTM5_MOUSE GLUTATHIONE S-TR ( 224) 460 107 1.7e-23 -gi|121765|sp|P21266|GTM3_HUMAN GLUTATHIONE S-TRA ( 225) 450 105 7.4e-23 -gi|1170096|sp|Q03013|GTM4_HUMAN GLUTATHIONE S-TR ( 218) 444 103 1.7e-22 -gi|121735|sp|P09488|GTM1_HUMAN GLUTATHIONE S-TRA ( 218) 444 103 1.7e-22 -gi|2506495|sp|P20136|GTM2_CHICK GLUTATHIONE S-TR ( 220) 431 101 1.2e-21 -gi|1170097|sp|P46439|GTM5_HUMAN GLUTATHIONE S-TR ( 218) 424 99 3.2e-21 -gi|232197|sp|P30112|GT26_FASHE GLUTATHIONE S-TRA ( 218) 333 80 1.8e-15 -gi|3915724|sp|P31671|GT28_FASHE GLUTATHIONE S-TR ( 218) 331 80 2.4e-15 -gi|3913799|sp|P56598|GT29_FASHE GLUTATHIONE S-TR ( 221) 326 79 5e-15 -gi|3915723|sp|P31670|GT27_FASHE GLUTATHIONE S-TR ( 218) 294 72 5.2e-13 -gi|544442|sp|P35661|GT27_SCHMA GLUTATHIONE S-TRA ( 218) 278 69 5.4e-12 -gi|121697|sp|P08515|GT26_SCHJA GLUTATHIONE S-TRA ( 218) 269 67 2e-11 -gi|121698|sp|P15964|GT26_SCHMA GLUTATHIONE S-TRA ( 218) 264 66 4.1e-11 -gi|1170095|sp|P46419|GTM1_DERPT GLUTATHIONE S-TR ( 219) 253 63 2.1e-10 -gi|121746|sp|P09211|GTP_HUMAN GLUTATHIONE S-TRAN ( 210) 209 54 1.2e-07 -gi|121747|sp|P19157|GTP1_MOUSE GLUTATHIONE S-TRA ( 210) 209 54 1.2e-07 -gi|1170100|sp|P46424|GTP_CRILO GLUTATHIONE S-TRA ( 210) 209 54 1.2e-07 -gi|1346208|sp|P47954|GTP_CRIMI GLUTATHIONE S-TRA ( 210) 207 54 1.6e-07 -gi|121744|sp|P28801|GTP_BOVIN GLUTATHIONE S-TRAN ( 210) 205 53 2.1e-07 -gi|1170099|sp|P46425|GTP2_MOUSE GLUTATHIONE S-TR ( 210) 200 52 4.4e-07 -gi|3023905|sp|Q60550|GTP_MESAU GLUTATHIONE S-TRA ( 210) 200 52 4.4e-07 -gi|544445|sp|P80031|GTP_PIG GLUTATHIONE S-TRANSF ( 207) 199 52 5.1e-07 -gi|2495108|sp|Q28514|GTP_MACMU GLUTATHIONE S-TRA ( 210) 197 52 6.9e-07 -gi|121749|sp|P04906|GTP_RAT GLUTATHIONE S-TRANSF ( 210) 185 49 3.9e-06 -gi|1170102|sp|P46427|GTP_ONCVO GLUTATHIONE S-TRA ( 208) 174 47 1.9e-05 -gi|1170101|sp|P46426|GTP_DIRIM GLUTATHIONE S-TRA ( 208) 173 47 2.2e-05 -gi|121745|sp|P10299|GTP_CAEEL GLUTATHIONE S-TRAN ( 208) 167 45 5.4e-05 -gi|6225842|sp|O73888|PGD_CHICK GLUTATHIONE-REQUI ( 199) 103 32 0.58 -gi|134261|sp|P18426|SC11_OMMSL S-CRYSTALLIN SL11 ( 205) 99 31 1.1 -gi|6226954|sp|O35543|PGD_RAT GLUTATHIONE-REQUIRI ( 199) 98 31 1.2 -gi|116006|sp|P08575|CD45_HUMAN LEUKOCYTE COMMON (1304) 105 33 1.8 -gi|6225843|sp|O60760|PGD_HUMAN GLUTATHIONE-REQUI ( 199) 95 30 1.8 -gi|2496132|sp|Q58248|Y838_METJA HYPOTHETICAL PRO ( 223) 91 29 3.6 -gi|1351503|sp|P47431|Y185_MYCGE HYPOTHETICAL LIP ( 701) 96 31 4.2 -gi|585954|sp|P26864|RT02_MARPO MITOCHONDRIAL RIB ( 237) 90 29 4.4 -gi|1175586|sp|P44135|YC46_HAEIN HYPOTHETICAL PRO ( 647) 92 30 7.1 -gi|121696|sp|P28338|GTT1_MUSDO GLUTATHIONE S-TRA ( 208) 86 28 7.1 -gi|1175976|sp|P43589|YFH5_YEAST HYPOTHETICAL 52. ( 448) 89 29 8.2 -gi|549012|sp|Q06182|SW10_SCHPO MATING-TYPE SWITC ( 252) 85 28 9.5 - - -119 residues in 1 query sequences -34569641 residues in 94745 library sequences - Tcomplib (2 proc)[33t08] - start: Sat Apr 7 11:05:45 2001 done: Sat Apr 7 11:11:13 2001 - Scan time: 1.010 Display time: 0.290 - -Function used was FASTA [version 3.3t08d4 Mar. 27, 2001] -done -starting fastxy33_t Sat Apr 7 11:11:13 EDT 2001 -done -starting fastxy33_t rev Sat Apr 7 11:14:25 EDT 2001 -done -starting ssearch33_t Sat Apr 7 11:22:24 EDT 2001 -done -starting fasta33_t - DNA Sat Apr 7 11:26:08 EDT 2001 -done -starting tfasta33_t Sat Apr 7 11:39:50 EDT 2001 -done -starting tfastxy33_t Sat Apr 7 11:40:54 EDT 2001 -done -starting fastf33_t Sat Apr 7 12:41:29 EDT 2001 -done -starting tfastf33_t Sat Apr 7 12:42:05 EDT 2001 -done -starting fasts33_t Sat Apr 7 12:46:56 EDT 2001 -done -starting tfasts33_t Sat Apr 7 12:47:01 EDT 2001 -done -starting fasta33 - protein Sat Apr 7 12:47:34 EDT 2001 -done -starting fastx3 Sat Apr 7 12:48:38 EDT 2001 -done -starting fasty3 Sat Apr 7 12:51:22 EDT 2001 -done -starting fasta33 - DNA Sat Apr 7 12:54:34 EDT 2001 -done -starting ssearch3 Sat Apr 7 13:06:28 EDT 2001 -done -starting tfasta3 Sat Apr 7 13:19:33 EDT 2001 -done -starting tfastxy3 Sat Apr 7 13:21:38 EDT 2001 -done Sat Apr 7 13:28:41 EDT 2001 -starting prss3 Sat Apr 7 13:28:41 EDT 2001 - -***[prss33] Query sequence undefined*** - - PRSS compares a query sequence to shuffled sequences - using the Smith-Waterman algorithm - version 3.3t08d4 Mar. 27, 2001 -Please cite: - W.R. Pearson (1996) Meth. Enzymol. 266:227-258 - -done Sat Apr 7 13:28:46 EDT 2001 diff -ruN old/test.sh new/test.sh --- old/test.sh Wed Jun 30 10:37:31 2004 +++ new/test.sh Wed Jun 30 10:38:13 2004 @@ -7,7 +7,7 @@ fasta33_t -S -q -z 11 -O test_m1.ok2_t_p25 -s P250 mgstm1.aa:100-218 q echo "done" echo "starting fastxy33_t" `date` -fastx33_t -m 9 -S -q mgtt2_x.seq q > test_t2.xk2_t +fastx33_t -m 9 -S -q mgtt2_x.seq q 3 > test_t2.xk2_t fasty33_t -S -q mgtt2_x.seq q > test_t2.yk2_t fastx33_t -m 9 -S -q -z 2 mgstm1.esq a > test_m1.xk2_tz2 fasty33_t -S -q -z 2 mgstm1.esq a > test_m1.yk2_tz2 -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan
State Changed From-To: feedback->closed Committed, thanks. I have assigned the submitter as the new maintainer, since the current maintainer has not been responsive to PRs about his ports for some time.