Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-01 07:38:39 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 |
To the developers/maintainers of the DECIPHER package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 480/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DECIPHER 2.27.0 (landing page) Erik Wright
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | TIMEOUT | |||||||||
Package: DECIPHER |
Version: 2.27.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DECIPHER_2.27.0.tar.gz |
StartedAt: 2023-02-28 01:16:01 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 01:56:01 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 2400.1 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: DECIPHER.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DECIPHER_2.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DECIPHER.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘DECIPHER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DECIPHER’ version ‘2.27.0’ * 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 (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * checking installed package size ... NOTE installed size is 12.7Mb sub-directories of 1Mb or more: R 1.4Mb data 7.3Mb extdata 2.3Mb libs 1.3Mb * 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 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 ... NOTE 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 ‘deltaHrulesRNA’ TreeLine: multiple local function definitions for ‘.minimize’ with different formal arguments Undefined global functions or variables: 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 PredictDBN 147.213 0.392 147.615 MapCharacters 110.936 0.332 111.270 FindNonCoding 100.051 0.708 100.764 LearnNonCoding 72.805 3.624 76.436 BrowseSeqs 55.330 0.323 55.691 WriteGenes 51.264 0.136 51.400 ExtractGenes 50.150 0.412 50.565 FindGenes 48.886 0.820 49.707 Genes-class 48.358 0.196 48.556 AlignSeqs 26.703 0.472 27.176 CorrectFrameshifts 18.273 0.076 18.351 StaggerAlignment 16.728 0.188 16.918 LearnTaxa 15.005 0.608 15.614 AlignTranslation 14.556 0.124 14.682 Taxa-class 14.251 0.048 14.300 IdTaxa 12.965 0.056 13.022 DetectRepeats 12.694 0.060 12.756 TreeLine 10.311 0.108 10.420 Clusterize 7.409 0.040 7.449 ScoreAlignment 6.475 0.048 6.523 Array2Matrix 5.461 0.061 5.521 DesignArray 5.358 0.004 5.362 TileSeqs 5.259 0.000 5.259 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ArtOfAlignmentInR.Rnw’... OK ‘ClassifySequences.Rnw’... OK ‘ClusteringSequences.Rnw’... OK ‘DECIPHERing.Rnw’... OK ‘DesignMicroarray.Rnw’... OK ‘DesignPrimers.Rnw’... OK ‘DesignProbes.Rnw’... OK ‘DesignSignatures.Rnw’... OK ‘FindChimeras.Rnw’... OK ‘FindingGenes.Rnw’... OK ‘FindingNonCodingRNAs.Rnw’... OK ‘GrowingTrees.Rnw’... OK ‘RepeatRepeat.Rnw’... OK OK * checking re-building of vignette outputs ...
DECIPHER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DECIPHER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘DECIPHER’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:424:37: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 424 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:46: note: ‘lGp’ was declared here 61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c:426:37: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized] 426 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:51: 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:1266:37: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1266 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:808:46: note: ‘lGp’ was declared here 808 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c:1268:37: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1268 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:808:51: note: ‘lGs’ was declared here 808 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfiles’: AlignProfiles.c:378:25: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized] 378 | #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/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:463:49: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ CalculateDeltaG.c:463:36: 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/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:25:30: 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:31:30: 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:37:30: 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:43:30: 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:49:30: 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:55:30: 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/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:500:49: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized] 500 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:500:49: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:403:50: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 403 | minCs[i] = minC; | ~~~~~~~~~^~~~~~ Cluster.c:231:57: note: ‘minC’ was declared here 231 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster._omp_fn.1’: Cluster.c:427:72: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 427 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:231:57: note: ‘minC’ was declared here 231 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster’: Cluster.c:449:66: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 449 | rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged | ^ Cluster.c:739:37: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized] 739 | nDiv[i] = nDiv[i + 1]; | ^ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ClusterML.c -o ClusterML.o ClusterML.c:5666:13: warning: ‘L_unknown_5_SIMD’ defined but not used [-Wunused-function] 5666 | static void L_unknown_5_SIMD(double *__restrict Ls, const int i3, const int i1, const int i2, const double *P1, const double *P2, const double epsilon, const double inv_epsilon, const int root) | ^~~~~~~~~~~~~~~~ ClusterML.c:5064:13: warning: ‘L_unknown_SIMD’ defined but not used [-Wunused-function] 5064 | static void L_unknown_SIMD(double *__restrict Ls, const int i3, const int i1, const int i2, const double *P1, const double *P2, const double epsilon, const double inv_epsilon, const int root) | ^~~~~~~~~~~~~~ ClusterML.c: In function ‘clusterML’: ClusterML.c:6905:17: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized] 6905 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:38, from ClusterML.c:11: /home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:55:25: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized] 55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) | ^~~~~~~~~~ ClusterML.c:6737:17: note: ‘I’ was declared here 6737 | double *I; | ^ In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:38, from ClusterML.c:11: /home/biocbuild/bbs-3.17-bioc/R/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:6736:14: note: ‘Up’ was declared here 6736 | int *Up; | ^~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:72:22: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized] 72 | int i, j, k, m, w; | ^ ClusterMP.c:125:30: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized] 125 | int *P; | ^ ClusterMP.c: In function ‘clusterMP’: ClusterMP.c:540:17: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized] 540 | free(Up); | ^~~~~~~~ ClusterMP.c:113:17: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized] 113 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:113:17: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized] ClusterMP.c:113:17: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c CommonGaps.c -o CommonGaps.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Compositions.c -o Compositions.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:976:52: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 976 | p[c] = ((k - 1) >> 8) & 0xFF; // length of run | ~~~^~~~ Compression.c:516:19: note: ‘k’ was declared here 516 | int i, j, k, pos; | ^ Compression.c:1010:54: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1010 | count++; | ~~~~~^~ Compression.c:542:43: note: ‘count’ was declared here 542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~ Compression.c:1009:62: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1009 | word = (word << 8) | (unsigned int)reorder(byte); | ~~~~~~^~~~~ Compression.c:542:37: note: ‘word’ was declared here 542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1212:56: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1212 | p[c++] = rev==0 ? 254 : 255; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ Compression.c:543:41: note: ‘rev’ was declared here 543 | int lastTemp, currTemp, rev, len, len2, thresh = 1; | ^~~ Compression.c:556:21: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized] 556 | int lower = 0; | ^~~~~ Compression.c:1239:71: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1239 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) { | ~~~^~~~~~~~~~~~~~ Compression.c:629:26: note: ‘lastTriplet’ was declared here 629 | int run, lastTriplet, lastCase; | ^~~~~~~~~~~ Compression.c:1029:79: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1029 | lastHit = dict[(word >> k) & 0xFF]; | ^ Compression.c:542:31: note: ‘dict’ was declared here 542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:1578:17: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1578 | double *DBN, *s; | ^~~ ConsensusSequence.c: In function ‘consensusProfileAA’: ConsensusSequence.c:455:53: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized] 455 | *(runs + s) += weight; | ^~ ConsensusSequence.c:397:30: note: ‘lastPos’ was declared here 397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1; | ^~~~~~~ ConsensusSequence.c:1771:17: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1771 | double *HEC, *s; | ^~~ ConsensusSequence.c: In function ‘colScores’: ConsensusSequence.c:2040:48: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2040 | *(rans + k) += GO*(curr*total); | ~~~~~^~~~~~~ ConsensusSequence.c:2040:48: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized] ConsensusSequence.c:1939:27: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1939 | int do_DBN, n, l, d; | ^ ConsensusSequence.c:1938:17: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1938 | double *DBN, *s; | ^~~ ConsensusSequence.c: In function ‘colScoresAA’: ConsensusSequence.c:2177:48: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2177 | *(rans + k) += GO*(curr*total); | ~~~~~^~~~~~~ ConsensusSequence.c:2177:48: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized] ConsensusSequence.c:2076:27: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2076 | int do_HEC, n, l, d; | ^ ConsensusSequence.c:2075:17: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2075 | double *HEC, *s; | ^~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:70:27: 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:77:27: 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:84:34: 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:834:85: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 834 | cycles += lastCycle - thisCycle; | ~~~~~~~~~~^~~~~~~~~~~ DesignProbes.c:267:58: note: ‘lastCycle’ was declared here 267 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ DesignProbes.c:834:85: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 834 | cycles += lastCycle - thisCycle; | ~~~~~~~~~~^~~~~~~~~~~ DesignProbes.c:267:69: note: ‘thisCycle’ was declared here 267 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Diff.c -o Diff.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:756:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 756 | if (!ci) | ^~ DistanceMatrix.c:759:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 759 | while (i < ex) { | ^~~~~ DistanceMatrix.c:778:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 778 | if (!cj) | ^~ DistanceMatrix.c:781:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 781 | while (j < ey) { | ^~~~~ DistanceMatrix.c: In function ‘similarities._omp_fn.0’: DistanceMatrix.c:995:45: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized] 995 | (double)(OV + g)/(double)w1 < coverage && | ~~~~^~~~ DistanceMatrix.c:843:45: note: ‘OV’ was declared here 843 | int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r; | ^~ DistanceMatrix.c:1015:82: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1015 | rans[i] = (double)s/((double)(ov + count + g2)); | ~~~^~~~~~~ DistanceMatrix.c:843:41: note: ‘ov’ was declared here 843 | int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r; | ^~ DistanceMatrix.c:1000:44: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1000 | if (o == 1) { | ^ DistanceMatrix.c:843:60: note: ‘o’ was declared here 843 | int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r; | ^ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:315:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 315 | x = x + (x >> 4) & 0xF0F0F0F; | ~~^~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:381:35: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized] 381 | } else if (k==2) { | ^ FindFrameshifts.c:318:47: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized] 318 | if (C[k*rc + j*r + i] >= 0) { | ~^~ FindFrameshifts.c:370:43: 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/bbs-3.17-bioc/R/include/Rdefines.h:41, from FindFrameshifts.c:11: /home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:893:33: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 893 | #define eval Rf_eval | ^~~~~~~ FindFrameshifts.c:162:31: note: ‘utilsPackage’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41, from FindFrameshifts.c:11: /home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:893:33: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 893 | #define eval Rf_eval | ^~~~~~~ FindFrameshifts.c:162:14: note: ‘percentComplete’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ FindFrameshifts.c:468:40: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 468 | before = *rPercentComplete; | ~~~~~~~^~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:422:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 422 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:432:64: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized] 432 | score += codons[lastVal*64 + val]; | ~~~~~~~^~~ GeneFinding.c: In function ‘startCodonModel’: GeneFinding.c:791:48: 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:892:48: 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:973:59: 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:1059:59: 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:1131:59: 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:1216:59: 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:1286:49: 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:1289:81: 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:1379:59: 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:1496:59: 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:1598:59: 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:1712:59: 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:1826:56: 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:1913:56: 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:1990:77: 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:2090:77: 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:2307:56: 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:2419:48: 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:2520:48: 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:2578:59: 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/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c GetPools.c -o GetPools.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Import.c -o Import.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c InformationContent.c -o InformationContent.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c InsertGaps.c -o InsertGaps.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c IntDist.c -o IntDist.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:79:27: 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:88:27: 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:358:59: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized] 358 | *(rans + k + l*s) += 1; | ^~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c MultiMatch.c -o MultiMatch.o MultiMatch.c: In function ‘intMatchSelfOnce’: MultiMatch.c:871:28: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 871 | int i, j, k, temp, start = 0; | ^~~~~ MultiMatch.c: In function ‘matchOverlap._omp_fn.0’: MultiMatch.c:1033:45: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1033 | two != one) { | ~~~~^~~~~~ MultiMatch.c:1008:21: note: ‘one’ was declared here 1008 | int one, two; | ^~~ In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41, from MultiMatch.c:11: MultiMatch.c: In function ‘matchLists’: /home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:893:33: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 893 | #define eval Rf_eval | ^~~~~~~ MultiMatch.c:247:31: note: ‘utilsPackage’ was declared here 247 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41, from MultiMatch.c:11: /home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:893:33: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 893 | #define eval Rf_eval | ^~~~~~~ MultiMatch.c:247:14: note: ‘percentComplete’ was declared here 247 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ MultiMatch.c:330:40: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 330 | before = *rPercentComplete; | ~~~~~~~^~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c NNLS.c -o NNLS.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Order.c -o Order.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:469:39: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 469 | P2[i] = p2; | ~~~~~~^~~~ PairwiseAlignment.c:173:19: note: ‘p2’ was declared here 173 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:468:39: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 468 | P1[i] = p1; | ~~~~~~^~~~ PairwiseAlignment.c:173:14: note: ‘p1’ was declared here 173 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:473:39: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized] 473 | P4[i] = p4; | ~~~~~~^~~~ PairwiseAlignment.c:173:29: note: ‘p4’ was declared here 173 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:472:39: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized] 472 | P3[i] = p3; | ~~~~~~^~~~ PairwiseAlignment.c:173:24: note: ‘p3’ was declared here 173 | int *p1, *p2, *p3, *p4; | ^~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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:869:85: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 869 | range2[0] = nucs[pos[prev]];// + 1; | ^ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c PredictHEC.c -o PredictHEC.o PredictHEC.c: In function ‘predictHEC’: PredictHEC.c:255:25: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized] 255 | SET_VECTOR_ELT(ret, i, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictHEC.c:233:51: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized] 233 | states[j] = 'C'; | ~~~~~~~~~~^~~~~ PredictHEC.c:237:46: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized] 237 | *(rans + 3*j + 1) = E; | ~~~~~~~~~~~~^~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c RemoveGaps.c -o RemoveGaps.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ReplaceChars.c -o ReplaceChars.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c SphericalKmeans.c -o SphericalKmeans.o SphericalKmeans.c: In function ‘sphericalKmeans’: SphericalKmeans.c:117:25: warning: ‘b’ may be used uninitialized in this function [-Wmaybe-uninitialized] 117 | free(b); | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Translate.c -o Translate.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c VectorSums.c -o VectorSums.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/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 CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o SphericalKmeans.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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 | 0.057 | 0.007 | 0.064 | |
Add2DB | 0.325 | 0.012 | 0.340 | |
AdjustAlignment | 0.247 | 0.000 | 0.251 | |
AlignDB | 1.245 | 0.052 | 1.300 | |
AlignProfiles | 0.806 | 0.020 | 0.827 | |
AlignSeqs | 26.703 | 0.472 | 27.176 | |
AlignSynteny | 3.430 | 0.040 | 3.471 | |
AlignTranslation | 14.556 | 0.124 | 14.682 | |
AmplifyDNA | 0.000 | 0.003 | 0.003 | |
Array2Matrix | 5.461 | 0.061 | 5.521 | |
BrowseDB | 0.029 | 0.000 | 0.029 | |
BrowseSeqs | 55.330 | 0.323 | 55.691 | |
CalculateEfficiencyArray | 0.018 | 0.000 | 0.018 | |
CalculateEfficiencyFISH | 0.006 | 0.000 | 0.005 | |
CalculateEfficiencyPCR | 0.002 | 0.003 | 0.005 | |
Clusterize | 7.409 | 0.040 | 7.449 | |
Codec | 1.313 | 0.000 | 1.314 | |
ConsensusSequence | 0.212 | 0.003 | 0.217 | |
Cophenetic | 0.21 | 0.00 | 0.21 | |
CorrectFrameshifts | 18.273 | 0.076 | 18.351 | |
CreateChimeras | 0.941 | 0.004 | 0.944 | |
DB2Seqs | 0.012 | 0.006 | 0.019 | |
DesignArray | 5.358 | 0.004 | 5.362 | |
DesignPrimers | 0 | 0 | 0 | |
DesignProbes | 0.001 | 0.000 | 0.001 | |
DesignSignatures | 0.001 | 0.000 | 0.001 | |
DetectRepeats | 12.694 | 0.060 | 12.756 | |
DigestDNA | 0.186 | 0.000 | 0.186 | |
Disambiguate | 0.066 | 0.000 | 0.066 | |
DistanceMatrix | 0.048 | 0.000 | 0.049 | |
ExtractGenes | 50.150 | 0.412 | 50.565 | |
FindChimeras | 0.089 | 0.000 | 0.089 | |
FindGenes | 48.886 | 0.820 | 49.707 | |
FindNonCoding | 100.051 | 0.708 | 100.764 | |
FindSynteny | 1.772 | 0.004 | 1.776 | |
FormGroups | 0.06 | 0.00 | 0.06 | |
Genes-class | 48.358 | 0.196 | 48.556 | |
HEC_MI | 0.236 | 0.000 | 0.236 | |
IdConsensus | 0.893 | 0.008 | 0.901 | |
IdLengths | 0.022 | 0.000 | 0.022 | |
IdTaxa | 12.965 | 0.056 | 13.022 | |
IdentifyByRank | 0.031 | 0.000 | 0.030 | |
LearnNonCoding | 72.805 | 3.624 | 76.436 | |
LearnTaxa | 15.005 | 0.608 | 15.614 | |
MIQS | 0.038 | 0.012 | 0.051 | |
MODELS | 0.002 | 0.000 | 0.002 | |
MapCharacters | 110.936 | 0.332 | 111.270 | |
MaskAlignment | 0.607 | 0.003 | 0.610 | |
MeltDNA | 0.053 | 0.000 | 0.054 | |
NNLS | 0.004 | 0.000 | 0.005 | |
NonCoding-class | 0.054 | 0.004 | 0.059 | |
NonCodingRNA | 0.104 | 0.000 | 0.104 | |
OrientNucleotides | 0.999 | 0.008 | 1.007 | |
PFASUM | 0.033 | 0.000 | 0.034 | |
PredictDBN | 147.213 | 0.392 | 147.615 | |
PredictHEC | 0.263 | 0.008 | 0.271 | |
RESTRICTION_ENZYMES | 0.001 | 0.002 | 0.003 | |
ReadDendrogram | 0.064 | 0.001 | 0.065 | |
RemoveGaps | 0.014 | 0.000 | 0.015 | |
ScoreAlignment | 6.475 | 0.048 | 6.523 | |
SearchDB | 0.041 | 0.000 | 0.041 | |
Seqs2DB | 0.102 | 0.004 | 0.107 | |
StaggerAlignment | 16.728 | 0.188 | 16.918 | |
Synteny-class | 2.661 | 0.004 | 2.665 | |
Taxa-class | 14.251 | 0.048 | 14.300 | |
TerminalChar | 0.016 | 0.000 | 0.015 | |
TileSeqs | 5.259 | 0.000 | 5.259 | |
TrainingSet_16S | 2.663 | 0.004 | 2.666 | |
TreeLine | 10.311 | 0.108 | 10.420 | |
TrimDNA | 0.184 | 0.004 | 0.188 | |
WriteDendrogram | 0.005 | 0.000 | 0.005 | |
WriteGenes | 51.264 | 0.136 | 51.400 | |
deltaGrules | 0.011 | 0.000 | 0.011 | |
deltaHrules | 0.019 | 0.000 | 0.019 | |
deltaHrulesRNA | 0.018 | 0.000 | 0.019 | |
deltaSrules | 0.062 | 0.004 | 0.066 | |
deltaSrulesRNA | 0.017 | 0.000 | 0.017 | |