Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-12 11:49 -0400 (Thu, 12 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4713 |
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 513/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DECIPHER 3.1.4 (landing page) Erik Wright
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the DECIPHER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DECIPHER.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: DECIPHER |
Version: 3.1.4 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DECIPHER_3.1.4.tar.gz |
StartedAt: 2024-09-12 04:12:30 -0000 (Thu, 12 Sep 2024) |
EndedAt: 2024-09-12 04:33:58 -0000 (Thu, 12 Sep 2024) |
EllapsedTime: 1288.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DECIPHER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DECIPHER_3.1.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DECIPHER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DECIPHER’ version ‘3.1.4’ * 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 ‘DECIPHER’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 13.7Mb sub-directories of 1Mb or more: R 1.4Mb data 7.5Mb extdata 2.5Mb libs 1.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 loading without being on the library search path ... 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 ... NOTE AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’ DesignSignatures: no visible binding for global variable ‘deltaHrules’ FindGenes: no visible binding for global variable ‘deltaHrulesRNA’ FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’ LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’ PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’ TreeLine: multiple local function definitions for ‘.minimize’ with different formal arguments Undefined global functions or variables: deltaGrulesRNA deltaHrules deltaHrulesRNA * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AlignSeqs 242.933 0.935 244.294 LearnNonCoding 138.091 1.474 139.751 MapCharacters 138.643 0.425 139.360 FindNonCoding 109.257 0.487 112.965 WriteGenes 63.943 0.096 64.168 ExtractGenes 63.786 0.175 64.088 FindGenes 61.674 0.056 61.841 Genes-class 61.619 0.084 61.804 BrowseSeqs 29.844 0.096 29.999 CorrectFrameshifts 20.997 0.080 21.113 LearnTaxa 18.536 0.270 18.837 DetectRepeats 17.395 0.080 17.511 StaggerAlignment 16.315 0.119 16.494 AlignTranslation 15.949 0.051 16.033 TreeLine 12.711 0.024 12.764 Taxa-class 12.620 0.048 12.691 IdTaxa 11.606 0.008 11.635 Clusterize 7.557 0.032 7.604 ScoreAlignment 7.099 0.068 7.182 Array2Matrix 5.368 0.056 5.434 DesignArray 5.229 0.008 5.246 TileSeqs 5.042 0.000 5.052 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck/00check.log’ for details.
DECIPHER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DECIPHER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘DECIPHER’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c AlignProfiles.c -o AlignProfiles.o AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’: AlignProfiles.c:435:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 435 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:39: note: ‘lGp’ was declared here 61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c:437:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized] 437 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:44: note: ‘lGs’ was declared here 61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’: AlignProfiles.c:1288:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1288 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:819:39: note: ‘lGp’ was declared here 819 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c:1290:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1290 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:819:44: note: ‘lGs’ was declared here 819 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfiles’: AlignProfiles.c:388:11: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized] 388 | #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(NTHREADS) | ^~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o CalculateDeltaG.c: In function ‘calculateHairpinDeltaG’: CalculateDeltaG.c:463:28: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ CalculateDeltaG.c:463:15: warning: ‘s1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c CalculateFISH.c -o CalculateFISH.o CalculateFISH.c: In function ‘calculateFISH’: CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces] 25 | double dH_DR[4][4] = { | ^ 26 | -11.5, -7.8, -7, -8.3, | { } 27 | -10.4, -12.8, -16.3, -9.1, | { } 28 | -8.6, -8, -9.3, -5.9, | { } 29 | -7.8, -5.5, -9, -7.8 | { 30 | }; | } CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces] 31 | double dS_DR[4][4] = { | ^ 32 | -36.4, -21.6, -19.7, -23.9, | { } 33 | -28.4, -31.9, -47.1, -23.5, | { } 34 | -22.9, -17.1, -23.2, -12.3, | { } 35 | -23.2, -13.5, -26.1, -21.9 | { 36 | }; | } CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces] 37 | double dH_DD[4][4] = { | ^ 38 | -7.9, -8.4, -7.8, -7.2, | { } 39 | -8.5, -8, -10.6, -7.8, | { } 40 | -8.2, -9.8, -8, -8.4, | { } 41 | -7.2, -8.2, -8.5, -7.9 | { 42 | }; | } CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces] 43 | double dS_DD[4][4] = { | ^ 44 | -22.2, -22.4, -21, -20.4, | { } 45 | -22.7, -19.9, -27.2, -21, | { } 46 | -22.2, -24.4, -19.9, -22.4, | { } 47 | -21.3, -22.2, -22.7, -22.2 | { 48 | }; | } CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces] 49 | double dH_RR[4][4] = { | ^ 50 | -6.6, -10.17, -7.65, -5.76, | { } 51 | -10.56, -12.21, -7.95, -7.65, | { } 52 | -13.37, -14.21, -12.21, -10.17, | { } 53 | -8.11, -13.37, -10.56, -6.6 | { 54 | }; | } CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces] 55 | double dS_RR[4][4] = { | ^ 56 | -18.38, -26.03, -19.18, -15.67, | { } 57 | -28.25, -30.02, -19.18, -19.18, | { } 58 | -35.68, -34.85, -30.02, -26.03, | { } 59 | -22.59, -35.68, -28.25, -18.38 | { 60 | }; | } gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ChainSegments.c -o ChainSegments.o ChainSegments.c: In function ‘chainSegments’: ChainSegments.c:524:28: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized] 524 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:524:28: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Cluster.c -o Cluster.o Cluster.c: In function ‘cluster._omp_fn.0’: Cluster.c:418:15: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 418 | minCs[i] = minC; | ~~~~~~~~~^~~~~~ Cluster.c:246:50: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster._omp_fn.1’: Cluster.c:442:30: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 442 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:50: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster’: Cluster.c:464:52: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 464 | rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged | ^ Cluster.c:781:13: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized] 781 | nDiv[j] -= dMatrix2[length*colIndices[j] - colIndices[j]*(colIndices[j] + 1)/2 + rowIndices[i] - colIndices[j]]; // col sums | ^~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ClusterML.c -o ClusterML.o In file included from /home/biocbuild/R/R-4.4.1/include/Rdefines.h:38, from ClusterML.c:16: ClusterML.c: In function ‘clusterML’: /home/biocbuild/R/R-4.4.1/include/R_ext/RS.h:55:25: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized] 55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) | ^~~~~~~~~~ ClusterML.c:1206:7: note: ‘Up’ was declared here 1206 | int *Up; | ^~ ClusterML.c:1293:10: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1293 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ClusterMP.c -o ClusterMP.o ClusterMP.c: In function ‘clusterMP._omp_fn.0’: ClusterMP.c:98:15: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized] 98 | int i, j, k, m, w; | ^ ClusterMP.c:153:9: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized] 153 | int *P; | ^ ClusterMP.c: In function ‘clusterMP’: ClusterMP.c:640:3: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized] 640 | free(Up); | ^~~~~~~~ ClusterMP.c:140:10: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:140:10: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized] ClusterMP.c:140:10: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Compositions.c -o Compositions.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Compression.c -o Compression.o Compression.c: In function ‘nbit._omp_fn.0’: Compression.c:978:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 978 | p[c] = ((k - 1) >> 8) & 0xFF; // length of run | ~~~^~~~ Compression.c:516:12: note: ‘k’ was declared here 516 | int i, j, k, pos; | ^ Compression.c:1012:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1012 | count++; | ~~~~~^~ Compression.c:544:29: note: ‘count’ was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~ Compression.c:1011:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1011 | word = (word << 8) | (unsigned int)reorder(byte); | ~~~~~~^~~~~ Compression.c:544:23: note: ‘word’ was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1214:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1214 | p[c++] = rev == 0 ? 254 : 255; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ Compression.c:545:27: note: ‘rev’ was declared here 545 | int lastTemp, currTemp, rev, len, len2, thresh = 1; | ^~~ Compression.c:558:7: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized] 558 | int lower = 0; | ^~~~~ Compression.c:1241:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1241 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) { | ~~~^~~~~~~~~~~~~~ Compression.c:631:12: note: ‘lastTriplet’ was declared here 631 | int run, lastTriplet, lastCase; | ^~~~~~~~~~~ Compression.c:1031:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1031 | lastHit = dict[(word >> k) & 0xFF]; | ^ Compression.c:544:17: note: ‘dict’ was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o ConsensusSequence.c: In function ‘consensusProfile’: ConsensusSequence.c:1578:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1578 | double *DBN, *s; | ^~~ ConsensusSequence.c: In function ‘consensusProfileAA’: ConsensusSequence.c:455:18: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized] 455 | *(runs + s) += weight; | ^~ ConsensusSequence.c:397:23: note: ‘lastPos’ was declared here 397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1; | ^~~~~~~ ConsensusSequence.c:1771:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1771 | double *HEC, *s; | ^~~ ConsensusSequence.c: In function ‘colScores’: ConsensusSequence.c:2046:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2046 | *(rans + k) += GO*(curr*total); | ~~~~~^~~~~~~ ConsensusSequence.c:2046:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized] ConsensusSequence.c:1941:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1941 | int do_DBN, n, l, d; | ^ ConsensusSequence.c:1940:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1940 | double *DBN, *s; | ^~~ ConsensusSequence.c: In function ‘colScoresAA’: ConsensusSequence.c:2189:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2189 | *(rans + k) += GO*(curr*total); | ~~~~~^~~~~~~ ConsensusSequence.c:2189:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized] ConsensusSequence.c:2084:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2084 | int do_HEC, n, l, d; | ^ ConsensusSequence.c:2083:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2083 | double *HEC, *s; | ^~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c DesignProbes.c -o DesignProbes.o DesignProbes.c: In function ‘designProbes’: DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces] 70 | double NN[4][4] = { | ^ 71 | -0.816507461,-2.5401714,-1.647430026,-1.184658548 | { 72 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026 | }{ 73 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714 | }{ 74 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461 | }{ 75 | }; | } DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces] 77 | double PM[4][4] = { | ^ 78 | -0.141370102,-0.439805276,-0.285236035,-0.205111781 | { 79 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035 | }{ 80 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276 | }{ 81 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102 | }{ 82 | }; | } DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces] 84 | double sMM[4][5][5][4] = { | ^ 85 | 0,0,0,0 | {{{ 86 | ,1.545032445,1.254355018,1.491691514,1.329138183 | }{ 87 | ,1.150635633,0.582415494,1.075877275,1.187937642 | }{ 88 | ,1.203555051,1.001540513,0.864287715,0.717125848 | }{ 89 | ,0.75,0.65,0.69,0.78 | }{ 90 | ,0.630005348,0.18553379,0.730763505,0.709272397 | - | }},{{ 91 | ,0,0,0,0 | }{ 92 | ,0.856582783,-0.143236405,0.716721488,0.603652831 | }{ 93 | ,0.851622883,0.653168672,0.676545316,1.187937642 | }{ 94 | ,0.75,0.65,0.69,0.78 | }{ 95 | ,1.231861002,0.746214538,1.087821916,0.989140748 | - | }},{{ 96 | ,1.822113278,1.270687029,1.336192565,1.364584949 | }{ 97 | ,0,0,0,0 | }{ 98 | ,1.443665704,1.385046493,1.256013166,1.329138183 | }{ 99 | ,0.75,0.65,0.69,0.78 | }{ 100 | ,1.478009492,0.882097231,1.20450984,1.061002478 | - | }},{{ 101 | ,1.496720812,0.846496194,0.967868114,0.989140748 | }{ 102 | ,0.766581547,-0.024857805,0.50754303,0.709272397 | }{ 103 | ,0,0,0,0 | }{ 104 | ,0.75,0.65,0.69,0.78 | }{ 105 | ,0.75,0.65,0.69,0.78 | - | }},{{ 106 | ,0.75,0.65,0.69,0.78 | }{ 107 | ,0.75,0.65,0.69,0.78 | }{ 108 | ,0.76,0.65,0.69,0.78 | }{ 109 | ,0,0,0,0 | }{ 110 | ,0,0,0,0 | - | }}},{{{ 111 | ,1.295827995,0.84547091,0.91019099,1.256013166 | }{ 112 | ,0.755889609,0.241428373,0.396379912,0.676545316 | }{ 113 | ,0.99945386,0.740323132,0.435659206,0.864287715 | }{ 114 | ,0.65,0.55,0.48,0.69 | }{ 115 | ,0.843147406,0.101248351,0.49063599,0.50754303 | - | }},{{ 116 | ,0,0,0,0 | }{ 117 | ,1.0651638,0.249934344,0.699352949,0.716721488 | }{ 118 | ,0.871921533,0.59458138,0.396379912,1.075877275 | }{ 119 | ,0.65,0.56,0.49,0.69 | }{ 120 | ,1.07531714,0.318907854,0.653287717,0.967868114 | - | }},{{ 121 | ,1.099899195,0.730184613,0.661798984,1.336192565 | }{ 122 | ,0,0,0,0 | }{ 123 | ,1.45897431,1.318532145,0.91019099,1.491691514 | }{ 124 | ,0.65,0.56,0.49,0.69 | }{ 125 | ,1.242135174,0.894838095,1.108555445,1.20450984 | - | }},{{ 126 | ,0.911428974,0.524430101,0.653287717,1.087821916 | }{ 127 | ,0.503209827,0.274849491,0.49063599,0.730763505 | }{ 128 | ,0,0,0,0 | }{ 129 | ,0.65,0.55,0.48,0.69 | }{ 130 | ,0.65,0.55,0.48,0.69 | - | }},{{ 131 | ,0.65,0.56,0.49,0.69 | }{ 132 | ,0.65,0.56,0.49,0.69 | }{ 133 | ,0.65,0.55,0.48,0.69 | }{ 134 | ,0,0,0,0 | }{ 135 | ,0,0,0,0 | - | }}},{{{ 136 | ,1.100661785,0.969784756,1.318532145,1.385046493 | }{ 137 | ,0.565895968,-0.060347902,0.59458138,0.653168672 | }{ 138 | ,0.782168488,0.788161238,0.740323132,1.001540513 | }{ 139 | ,0.68,0.46,0.55,0.65 | }{ 140 | ,0.468913405,-0.469855984,0.274849491,-0.024857805 | - | }},{{ 141 | ,0,0,0,0 | }{ 142 | ,0.258195131,-0.70438632,0.249934344,-0.143236405 | }{ 143 | ,0.502914193,-0.060347902,0.241428373,0.582415494 | }{ 144 | ,0.68,0.47,0.56,0.65 | }{ 145 | ,0.584083861,0.258975454,0.524430101,0.846496194 | - | }},{{ 146 | ,0.968040559,0.797499702,0.730184613,1.270687029 | }{ 147 | ,0,0,0,0 | }{ 148 | ,1.081040749,0.969784756,0.84547091,1.254355018 | }{ 149 | ,0.68,0.47,0.56,0.65 | }{ 150 | ,1.048553951,0.728354541,0.894838095,0.882097231 | - | }},{{ 151 | ,0.88611252,0.258975454,0.318907854,0.746214538 | }{ 152 | ,0.239520858,-0.469855984,0.101248351,0.18553379 | }{ 153 | ,0,0,0,0 | }{ 154 | ,0.68,0.46,0.55,0.65 | }{ 155 | ,0.68,0.46,0.55,0.65 | - | }},{{ 156 | ,0.68,0.47,0.56,0.65 | }{ 157 | ,0.68,0.47,0.56,0.65 | }{ 158 | ,0.68,0.46,0.55,0.65 | }{ 159 | ,0,0,0,0 | }{ 160 | ,0,0,0,0 | - | }}},{{{ 161 | ,1.566899704,1.081040749,1.45897431,1.443665704 | }{ 162 | ,0.976725675,0.502914193,0.871921533,0.851622883 | }{ 163 | ,1.482046826,0.782168488,0.99945386,1.203555051 | }{ 164 | ,0.85,0.68,0.65,0.76 | }{ 165 | ,0.798628781,0.239520858,0.503209827,0.766581547 | - | }},{{ 166 | ,0,0,0,0 | }{ 167 | ,1.141098246,0.258195131,1.0651638,0.856582783 | }{ 168 | ,0.976725675,0.565895968,0.755889609,1.150635633 | }{ 169 | ,0.85,0.68,0.65,0.75 | }{ 170 | ,1.125403302,0.88611252,0.911428974,1.496720812 | - | }},{{ 171 | ,1.68169282,0.968040559,1.099899195,1.822113278 | }{ 172 | ,0,0,0,0 | }{ 173 | ,1.566899704,1.100661785,1.295827995,1.545032445 | }{ 174 | ,0.85,0.68,0.65,0.75 | }{ 175 | ,1.35948517,1.048553951,1.242135174,1.478009492 | - | }},{{ 176 | ,1.125403302,0.584083861,1.07531714,1.231861002 | }{ 177 | ,0.798628781,0.468913405,0.843147406,0.630005348 | }{ 178 | ,0,0,0,0 | }{ 179 | ,0.85,0.68,0.65,0.75 | }{ 180 | ,0.85,0.68,0.65,0.75 | - | }},{{ 181 | ,0.85,0.68,0.65,0.75 | }{ 182 | ,0.85,0.68,0.65,0.75 | }{ 183 | ,0.85,0.68,0.65,0.75 | }{ 184 | ,0,0,0,0 | }{ 185 | }; | }}} DesignProbes.c: In function ‘designProbes._omp_fn.0’: DesignProbes.c:838:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 838 | cycles += lastCycle - thisCycle; | ~~~~~~~~~~^~~~~~~~~~~ DesignProbes.c:269:37: note: ‘lastCycle’ was declared here 269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ DesignProbes.c:838:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 838 | cycles += lastCycle - thisCycle; | ~~~~~~~~~~^~~~~~~~~~~ DesignProbes.c:269:48: note: ‘thisCycle’ was declared here 269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Diff.c -o Diff.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o DistanceMatrix.c: In function ‘firstSeqsPosEqual’: DistanceMatrix.c:796:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 796 | if (!ci) | ^~ DistanceMatrix.c:799:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 799 | while (i < ex) { | ^~~~~ DistanceMatrix.c:818:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 818 | if (!cj) | ^~ DistanceMatrix.c:821:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 821 | while (j < ey) { | ^~~~~ DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’: DistanceMatrix.c:1053:11: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1053 | two != one) { | ~~~~^~~~~~ DistanceMatrix.c:1028:8: note: ‘one’ was declared here 1028 | int one, two; | ^~~ DistanceMatrix.c:1340:19: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1340 | if (w1 - p1 + p2 > w2 - t2) { | ~~~~~~~~^~~~ DistanceMatrix.c:883:69: note: ‘p2’ was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1340:14: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1340 | if (w1 - p1 + p2 > w2 - t2) { | ~~~^~~~ DistanceMatrix.c:883:65: note: ‘p1’ was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1374:31: warning: ‘off’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:883:89: note: ‘off’ was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~~ DistanceMatrix.c:1374:31: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:883:85: note: ‘OV’ was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1379:42: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1379 | sim[i] = (double)pos/((double)(ov - g2)); | ~~~~^~~~~ DistanceMatrix.c:883:81: note: ‘ov’ was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1378:10: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1378 | if (o == 1) { | ^ DistanceMatrix.c:883:105: note: ‘o’ was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c EnumerateSequence.c -o EnumerateSequence.o EnumerateSequence.c: In function ‘pop’: EnumerateSequence.c:545:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 545 | x = x + (x >> 4) & 0xF0F0F0F; | ~~^~~~~~~~~~ EnumerateSequence.c: In function ‘enumerateSequence’: EnumerateSequence.c:358:10: warning: ‘tot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 358 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:358:10: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized] EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’: EnumerateSequence.c:955:10: warning: ‘tot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 955 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:955:10: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c FindFrameshifts.c -o FindFrameshifts.o FindFrameshifts.c: In function ‘findFrameshifts’: FindFrameshifts.c:381:14: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized] 381 | } else if (k == 2) { | ^ FindFrameshifts.c:318:19: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized] 318 | if (C[k*rc + j*r + i] >= 0) { | ~^~ FindFrameshifts.c:370:8: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized] 370 | i += B[k*rc + j*r + i]; | ~~^~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/include/Rdefines.h:41, from FindFrameshifts.c:11: /home/biocbuild/R/R-4.4.1/include/Rinternals.h:903:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 903 | #define eval Rf_eval | ^~~~~~~ FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/include/Rdefines.h:41, from FindFrameshifts.c:11: /home/biocbuild/R/R-4.4.1/include/Rinternals.h:903:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 903 | #define eval Rf_eval | ^~~~~~~ FindFrameshifts.c:162:7: note: ‘percentComplete’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ FindFrameshifts.c:468:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 468 | before = *rPercentComplete; | ~~~~~~~^~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c GeneFinding.c -o GeneFinding.o GeneFinding.c: In function ‘scoreCodonModel’: GeneFinding.c:422:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 422 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:432:29: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized] 432 | score += codons[lastVal*64 + val]; | ~~~~~~~^~~ GeneFinding.c: In function ‘startCodonModel’: GeneFinding.c:791:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 791 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreStartCodonModel’: GeneFinding.c:892:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 892 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘initialCodonModel’: GeneFinding.c:973:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 973 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreInitialCodonModel’: GeneFinding.c:1059:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1059 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘terminationCodonModel’: GeneFinding.c:1131:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1131 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreTerminationCodonModel’: GeneFinding.c:1216:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1216 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘getRegion’: GeneFinding.c:1286:23: warning: ‘x_i.length’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1286 | (s == 0 && j >= 0 && j + w <= x_i.length)) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ GeneFinding.c:1289:39: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1289 | seq[k] = getBaseLetterRC(x_i.ptr[j--]); | ^ GeneFinding.c: In function ‘autocorrelationModel’: GeneFinding.c:1379:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1379 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreAutocorrelationModel’: GeneFinding.c:1496:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1496 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘couplingModel’: GeneFinding.c:1598:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1598 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreCouplingModel’: GeneFinding.c:1712:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1712 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘nucleotideBiasModel’: GeneFinding.c:1826:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1826 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreNucleotideBiasModel’: GeneFinding.c:1913:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1913 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘upstreamMotifModel’: GeneFinding.c:1990:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1990 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]); | ^ GeneFinding.c: In function ‘scoreUpstreamMotifModel’: GeneFinding.c:2090:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2090 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]); | ^ GeneFinding.c: In function ‘scoreRunLengthModel’: GeneFinding.c:2307:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2307 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘stopCodonModel’: GeneFinding.c:2419:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2419 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreStopCodonModel’: GeneFinding.c:2520:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2520 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘codonFrequencies’: GeneFinding.c:2578:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2578 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c GetPools.c -o GetPools.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Import.c -o Import.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c InformationContent.c -o InformationContent.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c IntDist.c -o IntDist.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ManipulateXStringSet.c -o ManipulateXStringSet.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c MeltPolymer.c -o MeltPolymer.o MeltPolymer.c: In function ‘meltPolymer’: MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces] 79 | double dH[4][4] = { | ^ 80 | -7.9,-8.4,-7.8,-7.2 | { 81 | ,-8.5,-8.0,-10.6,-7.8 | }{ 82 | ,-8.2,-9.8,-8.0,-8.4 | }{ 83 | ,-7.2,-8.2,-8.5,-7.9 | }{ 84 | }; | } MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces] 88 | double dS[4][4] = { | ^ 89 | -22.2,-22.4,-21.0,-20.4 | { 90 | ,-22.7,-19.9,-27.2,-21.0 | }{ 91 | ,-22.2,-24.4,-19.9,-22.4 | }{ 92 | ,-21.3,-22.2,-22.7,-22.2 | }{ 93 | }; | } MeltPolymer.c:358:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized] 358 | *(rans + k + l*s) += 1; | ^~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c NNLS.c -o NNLS.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Order.c -o Order.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c PairwiseAlignment.c -o PairwiseAlignment.o PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’: PairwiseAlignment.c:472:11: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 472 | P2[i] = p2; | ~~~~~~^~~~ PairwiseAlignment.c:175:12: note: ‘p2’ was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:471:11: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 471 | P1[i] = p1; | ~~~~~~^~~~ PairwiseAlignment.c:175:7: note: ‘p1’ was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:476:11: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized] 476 | P4[i] = p4; | ~~~~~~^~~~ PairwiseAlignment.c:175:22: note: ‘p4’ was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:475:11: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized] 475 | P3[i] = p3; | ~~~~~~^~~~ PairwiseAlignment.c:175:17: note: ‘p3’ was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c: In function ‘alignPairs’: PairwiseAlignment.c:1107:10: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1107:10: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] PairwiseAlignment.c:1107:10: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c PredictDBN.c -o PredictDBN.o PredictDBN.c: In function ‘predictDBN’: PredictDBN.c:873:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 873 | range2[0] = nucs[pos[prev]];// + 1; | ^ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c PredictHEC.c -o PredictHEC.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Search.c -o Search.o Search.c: In function ‘searchIndex._omp_fn.0’: Search.c:515:12: warning: ‘s_j.length’ may be used uninitialized in this function [-Wmaybe-uninitialized] 515 | bound = s_j.length - 1; // right bound | ~~~~~~^~~~~~~~~~~~~~~~ Search.c:443:23: note: ‘s_j.length’ was declared here 443 | Chars_holder p_i, s_j; | ^~~ Search.c:443:23: warning: ‘s_j.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:449:9: warning: ‘maxLen’ may be used uninitialized in this function [-Wmaybe-uninitialized] 449 | int maxLen; // maximum observed length | ^~~~~~ Search.c: In function ‘searchIndex’: Search.c:969:5: warning: ‘ans3’ may be used uninitialized in this function [-Wmaybe-uninitialized] 969 | SET_VECTOR_ELT(ans3, k, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ Search.c:201:9: warning: ‘matrices’ may be used uninitialized in this function [-Wmaybe-uninitialized] 201 | int ***matrices; | ^~~~~~~~ Search.c:208:10: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:208:10: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘lkup_col’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘lkup_row’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘dS’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘sM’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Translate.c -o Translate.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Utils.c -o Utils.o In file included from /home/biocbuild/R/R-4.4.1/include/Rdefines.h:41, from Utils.c:16: Utils.c: In function ‘matchOrder’: /home/biocbuild/R/R-4.4.1/include/Rinternals.h:903:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 903 | #define eval Rf_eval | ^~~~~~~ Utils.c:333:24: note: ‘utilsPackage’ was declared here 333 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/include/Rdefines.h:41, from Utils.c:16: /home/biocbuild/R/R-4.4.1/include/Rinternals.h:903:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 903 | #define eval Rf_eval | ^~~~~~~ Utils.c:333:7: note: ‘percentComplete’ was declared here 333 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Utils.c:431:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 431 | before = *rPercentComplete; | ~~~~~~~^~~~~~~~~~~~~~~~~~~ Utils.c: In function ‘splitPartitions’: Utils.c:982:21: warning: ‘change’ may be used uninitialized in this function [-Wmaybe-uninitialized] 982 | } else if (change - j >= m && // large enough partition | ~~~~~~~^~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c VectorSums.c -o VectorSums.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-DECIPHER/00new/DECIPHER/libs ** R ** data ** 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 (DECIPHER)
DECIPHER.Rcheck/DECIPHER-Ex.timings
name | user | system | elapsed | |
AA_REDUCED | 0.055 | 0.004 | 0.059 | |
Add2DB | 0.844 | 0.056 | 0.905 | |
AdjustAlignment | 0.271 | 0.000 | 0.274 | |
AlignDB | 1.543 | 0.148 | 1.699 | |
AlignPairs | 4.151 | 0.266 | 4.430 | |
AlignProfiles | 1.174 | 0.047 | 1.222 | |
AlignSeqs | 242.933 | 0.935 | 244.294 | |
AlignSynteny | 3.852 | 0.000 | 3.860 | |
AlignTranslation | 15.949 | 0.051 | 16.033 | |
AmplifyDNA | 0.003 | 0.000 | 0.003 | |
Array2Matrix | 5.368 | 0.056 | 5.434 | |
BLOSUM | 0.017 | 0.000 | 0.016 | |
BrowseDB | 0.052 | 0.000 | 0.055 | |
BrowseSeqs | 29.844 | 0.096 | 29.999 | |
CalculateEfficiencyArray | 0.015 | 0.004 | 0.019 | |
CalculateEfficiencyFISH | 0.005 | 0.000 | 0.005 | |
CalculateEfficiencyPCR | 0.005 | 0.000 | 0.005 | |
Clusterize | 7.557 | 0.032 | 7.604 | |
Codec | 1.469 | 0.000 | 1.471 | |
ConsensusSequence | 0.229 | 0.000 | 0.229 | |
Cophenetic | 0.213 | 0.000 | 0.214 | |
CorrectFrameshifts | 20.997 | 0.080 | 21.113 | |
CreateChimeras | 1.050 | 0.004 | 1.055 | |
DB2Seqs | 0.031 | 0.007 | 0.038 | |
DesignArray | 5.229 | 0.008 | 5.246 | |
DesignPrimers | 0.012 | 0.000 | 0.012 | |
DesignProbes | 0.013 | 0.000 | 0.012 | |
DesignSignatures | 0.013 | 0.000 | 0.014 | |
DetectRepeats | 17.395 | 0.080 | 17.511 | |
DigestDNA | 0.206 | 0.002 | 0.210 | |
Disambiguate | 0.071 | 0.001 | 0.071 | |
DistanceMatrix | 0.064 | 0.000 | 0.064 | |
ExtractGenes | 63.786 | 0.175 | 64.088 | |
FindChimeras | 0.094 | 0.000 | 0.095 | |
FindGenes | 61.674 | 0.056 | 61.841 | |
FindNonCoding | 109.257 | 0.487 | 112.965 | |
FindSynteny | 2.085 | 0.012 | 2.102 | |
FormGroups | 0.074 | 0.000 | 0.074 | |
Genes-class | 61.619 | 0.084 | 61.804 | |
HEC_MI | 0.213 | 0.000 | 0.214 | |
IdConsensus | 0.538 | 0.012 | 0.551 | |
IdLengths | 0.041 | 0.000 | 0.041 | |
IdTaxa | 11.606 | 0.008 | 11.635 | |
IdentifyByRank | 0.042 | 0.000 | 0.043 | |
IndexSeqs | 1.211 | 0.000 | 1.213 | |
InvertedIndex-class | 0.648 | 0.004 | 0.653 | |
LearnNonCoding | 138.091 | 1.474 | 139.751 | |
LearnTaxa | 18.536 | 0.270 | 18.837 | |
MIQS | 0.044 | 0.004 | 0.047 | |
MMLSUM | 0.009 | 0.000 | 0.009 | |
MODELS | 0.000 | 0.002 | 0.002 | |
MapCharacters | 138.643 | 0.425 | 139.360 | |
MaskAlignment | 0.609 | 0.012 | 0.623 | |
MeltDNA | 0.074 | 0.000 | 0.074 | |
NNLS | 0.004 | 0.000 | 0.003 | |
NonCoding-class | 0.056 | 0.000 | 0.056 | |
NonCodingRNA | 0.101 | 0.000 | 0.100 | |
OrientNucleotides | 0.539 | 0.000 | 0.539 | |
PAM | 0.009 | 0.000 | 0.008 | |
PFASUM | 0.009 | 0.000 | 0.010 | |
PredictDBN | 0.009 | 0.002 | 0.010 | |
PredictHEC | 0.305 | 0.001 | 0.307 | |
RESTRICTION_ENZYMES | 0.000 | 0.003 | 0.002 | |
ReadDendrogram | 0.022 | 0.001 | 0.023 | |
RemoveGaps | 0.016 | 0.000 | 0.016 | |
ScoreAlignment | 7.099 | 0.068 | 7.182 | |
SearchDB | 0.067 | 0.004 | 0.070 | |
SearchIndex | 1.661 | 0.004 | 1.667 | |
Seqs2DB | 0.141 | 0.000 | 0.141 | |
StaggerAlignment | 16.315 | 0.119 | 16.494 | |
Synteny-class | 2.762 | 0.012 | 2.781 | |
Taxa-class | 12.620 | 0.048 | 12.691 | |
TerminalChar | 0.008 | 0.000 | 0.008 | |
TileSeqs | 5.042 | 0.000 | 5.052 | |
TrainingSet_16S | 2.517 | 0.016 | 2.542 | |
TreeLine | 12.711 | 0.024 | 12.764 | |
TrimDNA | 0.152 | 0.004 | 0.157 | |
WriteDendrogram | 0.004 | 0.000 | 0.004 | |
WriteGenes | 63.943 | 0.096 | 64.168 | |
deltaGrules | 0.012 | 0.000 | 0.011 | |
deltaGrulesRNA | 0.018 | 0.004 | 0.022 | |
deltaHrules | 0.019 | 0.000 | 0.019 | |
deltaHrulesRNA | 0.015 | 0.004 | 0.019 | |
deltaSrules | 0.094 | 0.000 | 0.094 | |
deltaSrulesRNA | 0.017 | 0.000 | 0.017 | |