Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 509/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DECIPHER 3.3.2 (landing page) Erik Wright
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 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. |
Package: DECIPHER |
Version: 3.3.2 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings DECIPHER_3.3.2.tar.gz |
StartedAt: 2024-12-23 23:50:39 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-24 00:11:47 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 1267.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DECIPHER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings DECIPHER_3.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/DECIPHER.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'DECIPHER/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DECIPHER' version '3.3.2' * 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 whether package 'DECIPHER' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * checking installed package size ... INFO installed size is 12.5Mb sub-directories of 1Mb or more: R 1.4Mb data 7.5Mb extdata 2.5Mb * 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 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 '.NNI' with different formal arguments 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 for x64 is not available File 'E:/biocbuild/bbs-3.21-bioc/R/library/DECIPHER/libs/x64/DECIPHER.dll': Found '_assert', possibly from 'assert' (C) Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AlignSeqs 207.64 7.30 215.05 LearnNonCoding 121.52 7.22 128.79 FindNonCoding 72.77 11.65 84.63 Treeline 76.01 2.09 78.12 FindGenes 70.90 2.82 73.82 ExtractGenes 70.67 2.50 73.34 Genes-class 63.80 2.75 66.75 WriteGenes 62.16 3.52 65.90 BrowseSeqs 36.86 1.42 38.38 DistanceMatrix 32.63 0.83 33.47 InferRecombination 26.53 0.64 27.17 CorrectFrameshifts 19.23 0.92 20.15 DetectRepeats 15.61 0.61 16.24 AlignTranslation 15.25 0.83 16.08 StaggerAlignment 14.19 1.58 15.76 Taxa-class 11.28 0.47 11.76 IdTaxa 10.41 0.68 11.07 LearnTaxa 6.96 2.02 8.98 Array2Matrix 8.70 0.06 8.77 DesignArray 7.47 0.06 7.53 Clusterize 7.01 0.25 7.28 ScoreAlignment 5.67 0.32 5.98 MapCharacters 4.61 0.44 5.14 * 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: 2 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/DECIPHER.Rcheck/00check.log' for details.
DECIPHER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL DECIPHER ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'DECIPHER' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AlignProfiles.c -o AlignProfiles.o AlignProfiles.c: In function 'alignProfiles._omp_fn.0': AlignProfiles.c:438:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized] 438 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:62:51: note: 'lGs' was declared here 62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c:436:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized] 436 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:62:46: note: 'lGp' was declared here 62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c: In function 'alignProfilesAA._omp_fn.0': AlignProfiles.c:1291:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized] 1291 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:820:51: note: 'lGs' was declared here 820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c:1289:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized] 1289 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:820:46: note: 'lGp' was declared here 820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c: In function 'alignProfiles': AlignProfiles.c:389:25: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized] 389 | #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(NTHREADS) | ^~~ AlignProfiles.c:82:17: note: 'subM' was declared here 82 | double *subM; | ^~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AssignIndels.c -o AssignIndels.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateDeltaG.c -o CalculateDeltaG.o CalculateDeltaG.c: In function 'calculateHairpinDeltaG': CalculateDeltaG.c:463:36: warning: 's1' may be used uninitialized [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ CalculateDeltaG.c:375:29: note: 's1' was declared here 375 | int i, j, k, count, s1, s2; | ^~ CalculateDeltaG.c:463:49: warning: 's2' may be used uninitialized [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ CalculateDeltaG.c:375:33: note: 's2' was declared here 375 | int i, j, k, count, s1, s2; | ^~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChainSegments.c -o ChainSegments.o ChainSegments.c: In function 'chainSegments': ChainSegments.c:525:49: warning: 'upY' may be used uninitialized [-Wmaybe-uninitialized] 525 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:491:93: note: 'upY' was declared here 491 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY; | ^~~ ChainSegments.c:525:49: warning: 'upX' may be used uninitialized [-Wmaybe-uninitialized] 525 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:491:88: note: 'upX' was declared here 491 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY; | ^~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Cluster.c -o Cluster.o Cluster.c: In function 'cluster._omp_fn.0': Cluster.c:439:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 439 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: 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:469:50: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 469 | minCs[i] = minC; | ~~~~~~~~~^~~~~~ Cluster.c:246:57: note: 'minC' was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function 'cluster._omp_fn.2': Cluster.c:493:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 493 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: 'minC' was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function 'cluster': Cluster.c:848:44: warning: 'minCols' may be used uninitialized [-Wmaybe-uninitialized] 848 | if (minCols[rowIndices[i]] == (minRow + 1)) { | ^ Cluster.c:277:14: note: 'minCols' was declared here 277 | int *minCols; | ^~~~~~~ Cluster.c:459:41: warning: 'nDiv' may be used uninitialized [-Wmaybe-uninitialized] 459 | #pragma omp parallel for private(i,j,minC,minH) schedule(guided) num_threads(nthreads) | ^~~ Cluster.c:283:17: note: 'nDiv' was declared here 283 | double *nDiv; | ^~~~ Cluster.c:413:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 413 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: 'minC' was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClusterME.c -o ClusterME.o ClusterME.c: In function 'clusterME': ClusterME.c:322:101: warning: 'LLRL' may be used uninitialized [-Wmaybe-uninitialized] 322 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac | ~~~~~^~~~~~ ClusterME.c:284:24: note: 'LLRL' was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:322:101: warning: 'LRRL' may be used uninitialized [-Wmaybe-uninitialized] 322 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac | ~~~~~^~~~~~ ClusterME.c:284:30: note: 'LRRL' was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:323:101: warning: 'LLRR' may be used uninitialized [-Wmaybe-uninitialized] 323 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc | ~~~~~^~~~~~ ClusterME.c:284:36: note: 'LLRR' was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:323:101: warning: 'LRRR' may be used uninitialized [-Wmaybe-uninitialized] 323 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc | ~~~~~^~~~~~ ClusterME.c:284:42: note: 'LRRR' was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClusterML.c -o ClusterML.o ClusterML.c: In function 'clusterML': ClusterML.c:2045:17: warning: 'node' may be used uninitialized [-Wmaybe-uninitialized] 2045 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ ClusterML.c:1913:17: note: 'node' was declared here 1913 | double *node; | ^~~~ ClusterML.c:2045:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] 2045 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ ClusterML.c:1959:14: note: 'Up' was declared here 1959 | int *Up; | ^~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClusterMP.c -o ClusterMP.o ClusterMP.c: In function 'clusterMP._omp_fn.0': ClusterMP.c:190:71: warning: 'temp_nodes' may be used uninitialized [-Wmaybe-uninitialized] 190 | temp_nodes[j] = 0; | ~~~~~~~~~~~~~~^~~ ClusterMP.c:163:34: note: 'temp_nodes' was declared here 163 | int *temp_subM, *temp_nodes; | ^~~~~~~~~~ ClusterMP.c:465:49: warning: 'temp_lengths' may be used uninitialized [-Wmaybe-uninitialized] 465 | *(temp_lengths + j) += *(S + w*c + m)*weight; | ^~~~~~~~~~~~~~~~~~~ ClusterMP.c:162:38: note: 'temp_lengths' was declared here 162 | double *temp_score, *temp_lengths; | ^~~~~~~~~~~~ ClusterMP.c:485:73: warning: 'temp_subM' may be used uninitialized [-Wmaybe-uninitialized] 485 | *(temp_subM + c*m + w - 1) += weight; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:163:22: note: 'temp_subM' was declared here 163 | int *temp_subM, *temp_nodes; | ^~~~~~~~~ ClusterMP.c:202:49: warning: 'P' may be used uninitialized [-Wmaybe-uninitialized] 202 | allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:185:38: note: 'P' was declared here 185 | int *P; | ^ ClusterMP.c:385:61: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized] 385 | *(R + 3*c*n + m) = 0; | ^ ClusterMP.c:105:22: note: 'm' was declared here 105 | int i, j, k, m, w; | ^ ClusterMP.c: In function 'clusterMP': ClusterMP.c:159:17: warning: 'lengths' may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:128:17: note: 'lengths' was declared here 128 | double *lengths, *score; | ^~~~~~~ ClusterMP.c:159:17: warning: 'nodes' may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:129:20: note: 'nodes' was declared here 129 | int size, *nodes, *subM; | ^~~~~ ClusterMP.c:159:17: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:129:28: note: 'subM' was declared here 129 | int size, *nodes, *subM; | ^~~~ ClusterMP.c:159:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:145:14: note: 'Up' was declared here 145 | int *Up; | ^~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compositions.c -o Compositions.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compression.c -o Compression.o Compression.c: In function 'nbit._omp_fn.0': Compression.c:1242:71: warning: 'lastTriplet' may be used uninitialized [-Wmaybe-uninitialized] 1242 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) { | ~~~^~~~~~~~~~~~~~ Compression.c:632:26: note: 'lastTriplet' was declared here 632 | int run, lastTriplet, lastCase; | ^~~~~~~~~~~ Compression.c:1012:62: warning: 'word' may be used uninitialized [-Wmaybe-uninitialized] 1012 | word = (word << 8) | (unsigned int)reorder(byte); | ~~~~~~^~~~~ Compression.c:545:37: note: 'word' was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1013:54: warning: 'count' may be used uninitialized [-Wmaybe-uninitialized] 1013 | count++; | ~~~~~^~ Compression.c:545:43: note: 'count' was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~ Compression.c:546:41: warning: 'rev' may be used uninitialized [-Wmaybe-uninitialized] 546 | int lastTemp, currTemp, rev, len, len2, thresh = 1; | ^~~ Compression.c:1216:58: warning: 'lastHit' may be used uninitialized [-Wmaybe-uninitialized] 1216 | p[c++] = (unsigned char)lastHit; | ^~~~~~~~~~~~~~~~~~~~~~ Compression.c:545:50: note: 'lastHit' was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConsensusSequence.c -o ConsensusSequence.o In function 'runsAA', inlined from 'consensusProfileAA' at ConsensusSequence.c:1836:3: ConsensusSequence.c:454:50: warning: 'lastPos' may be used uninitialized [-Wmaybe-uninitialized] 454 | if (lastGap < (s - 2)) // ensure continuity before the run | ~~~^~~~ ConsensusSequence.c: In function 'consensusProfileAA': ConsensusSequence.c:397:30: note: 'lastPos' was declared here 397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1; | ^~~~~~~ ConsensusSequence.c: In function 'colScores': ConsensusSequence.c:1940:17: warning: 'DBN' may be used uninitialized [-Wmaybe-uninitialized] 1940 | double *DBN, *s; | ^~~ ConsensusSequence.c:1941:27: warning: 'd' may be used uninitialized [-Wmaybe-uninitialized] 1941 | int do_DBN, n, l, d; | ^ ConsensusSequence.c:2043:19: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized] 2043 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:1930:37: note: 'curr' was declared here 1930 | double weight, total, prev, curr; | ^~~~ ConsensusSequence.c: In function 'colScoresAA': ConsensusSequence.c:2083:17: warning: 'HEC' may be used uninitialized [-Wmaybe-uninitialized] 2083 | double *HEC, *s; | ^~~ ConsensusSequence.c:2084:27: warning: 'd' may be used uninitialized [-Wmaybe-uninitialized] 2084 | int do_HEC, n, l, d; | ^ ConsensusSequence.c:2186:19: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized] 2186 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:2073:37: note: 'curr' was declared here 2073 | double weight, total, prev, curr; | ^~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DesignProbes.c -o DesignProbes.o DesignProbes.c: In function 'designProbes': DesignProbes.c:71:27: warning: missing braces around initializer [-Wmissing-braces] 71 | double NN[4][4] = { | ^ 72 | -0.816507461,-2.5401714,-1.647430026,-1.184658548 | { 73 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026 | }{ 74 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714 | }{ 75 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461 | }{ 76 | }; | } DesignProbes.c:78:27: warning: missing braces around initializer [-Wmissing-braces] 78 | double PM[4][4] = { | ^ 79 | -0.141370102,-0.439805276,-0.285236035,-0.205111781 | { 80 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035 | }{ 81 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276 | }{ 82 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102 | }{ 83 | }; | } DesignProbes.c:85:34: warning: missing braces around initializer [-Wmissing-braces] 85 | double sMM[4][5][5][4] = { | ^ 86 | 0,0,0,0 | {{{ 87 | ,1.545032445,1.254355018,1.491691514,1.329138183 | }{ 88 | ,1.150635633,0.582415494,1.075877275,1.187937642 | }{ 89 | ,1.203555051,1.001540513,0.864287715,0.717125848 | }{ 90 | ,0.75,0.65,0.69,0.78 | }{ 91 | ,0.630005348,0.18553379,0.730763505,0.709272397 | - | }},{{ 92 | ,0,0,0,0 | }{ 93 | ,0.856582783,-0.143236405,0.716721488,0.603652831 | }{ 94 | ,0.851622883,0.653168672,0.676545316,1.187937642 | }{ 95 | ,0.75,0.65,0.69,0.78 | }{ 96 | ,1.231861002,0.746214538,1.087821916,0.989140748 | - | }},{{ 97 | ,1.822113278,1.270687029,1.336192565,1.364584949 | }{ 98 | ,0,0,0,0 | }{ 99 | ,1.443665704,1.385046493,1.256013166,1.329138183 | }{ 100 | ,0.75,0.65,0.69,0.78 | }{ 101 | ,1.478009492,0.882097231,1.20450984,1.061002478 | - | }},{{ 102 | ,1.496720812,0.846496194,0.967868114,0.989140748 | }{ 103 | ,0.766581547,-0.024857805,0.50754303,0.709272397 | }{ 104 | ,0,0,0,0 | }{ 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 | ,0.75,0.65,0.69,0.78 | }{ 109 | ,0.76,0.65,0.69,0.78 | }{ 110 | ,0,0,0,0 | }{ 111 | ,0,0,0,0 | - | }}},{{{ 112 | ,1.295827995,0.84547091,0.91019099,1.256013166 | }{ 113 | ,0.755889609,0.241428373,0.396379912,0.676545316 | }{ 114 | ,0.99945386,0.740323132,0.435659206,0.864287715 | }{ 115 | ,0.65,0.55,0.48,0.69 | }{ 116 | ,0.843147406,0.101248351,0.49063599,0.50754303 | - | }},{{ 117 | ,0,0,0,0 | }{ 118 | ,1.0651638,0.249934344,0.699352949,0.716721488 | }{ 119 | ,0.871921533,0.59458138,0.396379912,1.075877275 | }{ 120 | ,0.65,0.56,0.49,0.69 | }{ 121 | ,1.07531714,0.318907854,0.653287717,0.967868114 | - | }},{{ 122 | ,1.099899195,0.730184613,0.661798984,1.336192565 | }{ 123 | ,0,0,0,0 | }{ 124 | ,1.45897431,1.318532145,0.91019099,1.491691514 | }{ 125 | ,0.65,0.56,0.49,0.69 | }{ 126 | ,1.242135174,0.894838095,1.108555445,1.20450984 | - | }},{{ 127 | ,0.911428974,0.524430101,0.653287717,1.087821916 | }{ 128 | ,0.503209827,0.274849491,0.49063599,0.730763505 | }{ 129 | ,0,0,0,0 | }{ 130 | ,0.65,0.55,0.48,0.69 | }{ 131 | ,0.65,0.55,0.48,0.69 | - | }},{{ 132 | ,0.65,0.56,0.49,0.69 | }{ 133 | ,0.65,0.56,0.49,0.69 | }{ 134 | ,0.65,0.55,0.48,0.69 | }{ 135 | ,0,0,0,0 | }{ 136 | ,0,0,0,0 | - | }}},{{{ 137 | ,1.100661785,0.969784756,1.318532145,1.385046493 | }{ 138 | ,0.565895968,-0.060347902,0.59458138,0.653168672 | }{ 139 | ,0.782168488,0.788161238,0.740323132,1.001540513 | }{ 140 | ,0.68,0.46,0.55,0.65 | }{ 141 | ,0.468913405,-0.469855984,0.274849491,-0.024857805 | - | }},{{ 142 | ,0,0,0,0 | }{ 143 | ,0.258195131,-0.70438632,0.249934344,-0.143236405 | }{ 144 | ,0.502914193,-0.060347902,0.241428373,0.582415494 | }{ 145 | ,0.68,0.47,0.56,0.65 | }{ 146 | ,0.584083861,0.258975454,0.524430101,0.846496194 | - | }},{{ 147 | ,0.968040559,0.797499702,0.730184613,1.270687029 | }{ 148 | ,0,0,0,0 | }{ 149 | ,1.081040749,0.969784756,0.84547091,1.254355018 | }{ 150 | ,0.68,0.47,0.56,0.65 | }{ 151 | ,1.048553951,0.728354541,0.894838095,0.882097231 | - | }},{{ 152 | ,0.88611252,0.258975454,0.318907854,0.746214538 | }{ 153 | ,0.239520858,-0.469855984,0.101248351,0.18553379 | }{ 154 | ,0,0,0,0 | }{ 155 | ,0.68,0.46,0.55,0.65 | }{ 156 | ,0.68,0.46,0.55,0.65 | - | }},{{ 157 | ,0.68,0.47,0.56,0.65 | }{ 158 | ,0.68,0.47,0.56,0.65 | }{ 159 | ,0.68,0.46,0.55,0.65 | }{ 160 | ,0,0,0,0 | }{ 161 | ,0,0,0,0 | - | }}},{{{ 162 | ,1.566899704,1.081040749,1.45897431,1.443665704 | }{ 163 | ,0.976725675,0.502914193,0.871921533,0.851622883 | }{ 164 | ,1.482046826,0.782168488,0.99945386,1.203555051 | }{ 165 | ,0.85,0.68,0.65,0.76 | }{ 166 | ,0.798628781,0.239520858,0.503209827,0.766581547 | - | }},{{ 167 | ,0,0,0,0 | }{ 168 | ,1.141098246,0.258195131,1.0651638,0.856582783 | }{ 169 | ,0.976725675,0.565895968,0.755889609,1.150635633 | }{ 170 | ,0.85,0.68,0.65,0.75 | }{ 171 | ,1.125403302,0.88611252,0.911428974,1.496720812 | - | }},{{ 172 | ,1.68169282,0.968040559,1.099899195,1.822113278 | }{ 173 | ,0,0,0,0 | }{ 174 | ,1.566899704,1.100661785,1.295827995,1.545032445 | }{ 175 | ,0.85,0.68,0.65,0.75 | }{ 176 | ,1.35948517,1.048553951,1.242135174,1.478009492 | - | }},{{ 177 | ,1.125403302,0.584083861,1.07531714,1.231861002 | }{ 178 | ,0.798628781,0.468913405,0.843147406,0.630005348 | }{ 179 | ,0,0,0,0 | }{ 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 | ,0.85,0.68,0.65,0.75 | }{ 185 | ,0,0,0,0 | }{ 186 | }; | }}} DesignProbes.c: In function 'designProbes._omp_fn.0': DesignProbes.c:838:60: warning: 'lastCycle' may be used uninitialized [-Wmaybe-uninitialized] 838 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:270:58: note: 'lastCycle' was declared here 270 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ DesignProbes.c:838:60: warning: 'thisCycle' may be used uninitialized [-Wmaybe-uninitialized] 838 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:270:69: note: 'thisCycle' was declared here 270 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Diff.c -o Diff.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DistanceMatrix.c -o DistanceMatrix.o DistanceMatrix.c: In function 'firstSeqsPosEqual': DistanceMatrix.c:1009:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1009 | if (!ci) | ^~ DistanceMatrix.c:1012:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1012 | while (i < ex) { | ^~~~~ DistanceMatrix.c:1031:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1031 | if (!cj) | ^~ DistanceMatrix.c:1034:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1034 | while (j < ey) { | ^~~~~ DistanceMatrix.c: In function 'computeOverlap._omp_fn.0': DistanceMatrix.c:1587:66: warning: 'OV' may be used uninitialized [-Wmaybe-uninitialized] 1587 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:1096:92: note: 'OV' was declared here 1096 | 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:1587:66: warning: 'off' may be used uninitialized [-Wmaybe-uninitialized] 1587 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:1096:96: note: 'off' was declared here 1096 | 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:1266:53: warning: 'one' may be used uninitialized [-Wmaybe-uninitialized] 1266 | two != one) { | ~~~~^~~~~~ DistanceMatrix.c:1241:29: note: 'one' was declared here 1241 | int one, two; | ^~~ DistanceMatrix.c:1603:52: warning: 'o' may be used uninitialized [-Wmaybe-uninitialized] 1603 | if (o == 1) { | ^ DistanceMatrix.c:1096:112: note: 'o' was declared here 1096 | 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:1606:91: warning: 'ov' may be used uninitialized [-Wmaybe-uninitialized] 1606 | sim[i] = (double)pos/((double)(ov + count + g2)); | ~~~^~~~~~~ DistanceMatrix.c:1096:88: note: 'ov' was declared here 1096 | 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; | ^~ In function 'distance', inlined from 'distMatrix._omp_fn.0' at DistanceMatrix.c:729:20: DistanceMatrix.c:391:17: warning: 'counts' may be used uninitialized [-Wmaybe-uninitialized] 391 | free(counts); | ^~~~~~~~~~~~ DistanceMatrix.c: In function 'distMatrix._omp_fn.0': DistanceMatrix.c:137:30: note: 'counts' was declared here 137 | int i, j, I, J, m2, *counts; | ^~~~~~ DistanceMatrix.c: In function 'distMatrix': DistanceMatrix.c:624:33: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized] 624 | #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads) | ^~~ DistanceMatrix.c:545:13: note: 'm' was declared here 545 | int m, *lkup_row, *lkup_col; | ^ DistanceMatrix.c:624:33: warning: 'lkup_row' may be used uninitialized [-Wmaybe-uninitialized] 624 | #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads) | ^~~ DistanceMatrix.c:545:17: note: 'lkup_row' was declared here 545 | int m, *lkup_row, *lkup_col; | ^~~~~~~~ DistanceMatrix.c:624:33: warning: 'lkup_col' may be used uninitialized [-Wmaybe-uninitialized] 624 | #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads) | ^~~ DistanceMatrix.c:545:28: note: 'lkup_col' was declared here 545 | int m, *lkup_row, *lkup_col; | ^~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EnumerateSequence.c -o EnumerateSequence.o EnumerateSequence.c: In function 'pop': EnumerateSequence.c:546:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 546 | x = x + (x >> 4) & 0xF0F0F0F; | ~~^~~~~~~~~~ EnumerateSequence.c: In function 'enumerateSequence': EnumerateSequence.c:359:17: warning: 'mN' may be used uninitialized [-Wmaybe-uninitialized] 359 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:318:14: note: 'mN' was declared here 318 | int *mN; | ^~ EnumerateSequence.c:359:17: warning: 'tot' may be used uninitialized [-Wmaybe-uninitialized] 359 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:319:13: note: 'tot' was declared here 319 | int tot; // total number of k-mers | ^~~ EnumerateSequence.c: In function 'enumerateSequenceReducedAA': EnumerateSequence.c:956:17: warning: 'mN' may be used uninitialized [-Wmaybe-uninitialized] 956 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:908:14: note: 'mN' was declared here 908 | int *mN; | ^~ EnumerateSequence.c:956:17: warning: 'tot' may be used uninitialized [-Wmaybe-uninitialized] 956 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:909:13: note: 'tot' was declared here 909 | int tot; // total number of k-mers | ^~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FindFrameshifts.c -o FindFrameshifts.o FindFrameshifts.c: In function 'findFrameshifts': FindFrameshifts.c:464:43: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 464 | *rPercentComplete = floor(100*(double)(s + 1)/f_length); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FindFrameshifts.c:160:25: note: 'rPercentComplete' was declared here 160 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from E:/biocbuild/bbs-3.21-bioc/R/include/Rdefines.h:41, from FindFrameshifts.c:11: E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:927:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 927 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro 'eval' 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:14: note: 'percentComplete' was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:927:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 927 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro 'eval' 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:31: note: 'utilsPackage' was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ FindFrameshifts.c:317:34: warning: 'I' may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:28: note: 'I' was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:317:43: warning: 'J' may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:31: note: 'J' was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:376:28: warning: 'K' may be used uninitialized [-Wmaybe-uninitialized] 376 | if (k == 1) { | ^ FindFrameshifts.c:135:34: note: 'K' was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GeneFinding.c -o GeneFinding.o GeneFinding.c: In function 'scoreCodonModel': GeneFinding.c:422:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 422 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:389:22: note: 'x_i.ptr' was declared here 389 | Chars_holder x_i; | ^~~ GeneFinding.c:432:57: warning: 'lastVal' may be used uninitialized [-Wmaybe-uninitialized] 432 | if (val < 64 && lastVal < 64) | ~~~~~~~~^~~~ GeneFinding.c:372:32: note: 'lastVal' was declared here 372 | int i, j, s, fin, val, lastVal, dicodon; | ^~~~~~~ GeneFinding.c: In function 'startCodonModel': GeneFinding.c:796:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 796 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:772:22: note: 'x_i.ptr' was declared here 772 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreStartCodonModel': GeneFinding.c:897:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 897 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:869:22: note: 'x_i.ptr' was declared here 869 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'initialCodonModel': GeneFinding.c:952:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 952 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:929:22: note: 'x_i.ptr' was declared here 929 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreInitialCodonModel': GeneFinding.c:1059:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1059 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1032:22: note: 'x_i.ptr' was declared here 1032 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'terminationCodonModel': GeneFinding.c:1116:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1116 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1093:22: note: 'x_i.ptr' was declared here 1093 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreTerminationCodonModel': GeneFinding.c:1216:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1216 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1189:22: note: 'x_i.ptr' was declared here 1189 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'getRegion': GeneFinding.c:1317:81: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1317 | seq[k] = getBaseLetterRC(x_i.ptr[j--]); | ^ GeneFinding.c:1253:22: note: 'x_i.ptr' was declared here 1253 | Chars_holder x_i; | ^~~ GeneFinding.c:1314:51: warning: 'x_i.length' may be used uninitialized [-Wmaybe-uninitialized] 1314 | (s == 0 && j >= 0 && j + w <= x_i.length)) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ GeneFinding.c:1253:22: note: 'x_i.length' was declared here 1253 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'autocorrelationModel': GeneFinding.c:1379:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1379 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1351:22: note: 'x_i.ptr' was declared here 1351 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreAutocorrelationModel': GeneFinding.c:1496:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1496 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1462:22: note: 'x_i.ptr' was declared here 1462 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'couplingModel': GeneFinding.c:1598:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1598 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1574:22: note: 'x_i.ptr' was declared here 1574 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreCouplingModel': GeneFinding.c:1712:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1712 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1682:22: note: 'x_i.ptr' was declared here 1682 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'nucleotideBiasModel': GeneFinding.c:1827:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1827 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1789:22: note: 'x_i.ptr' was declared here 1789 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreNucleotideBiasModel': GeneFinding.c:1914:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1914 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1883:22: note: 'x_i.ptr' was declared here 1883 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'upstreamMotifModel': GeneFinding.c:1993:75: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1993 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:1951:22: note: 'x_i.ptr' was declared here 1951 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreUpstreamMotifModel': GeneFinding.c:2093:75: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2093 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:2058:22: note: 'x_i.ptr' was declared here 2058 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreRunLengthModel': GeneFinding.c:2308:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2308 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2277:22: note: 'x_i.ptr' was declared here 2277 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'stopCodonModel': GeneFinding.c:2424:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2424 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:2400:22: note: 'x_i.ptr' was declared here 2400 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreStopCodonModel': GeneFinding.c:2525:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2525 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:2497:22: note: 'x_i.ptr' was declared here 2497 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'codonFrequencies': GeneFinding.c:2578:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2578 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2555:22: note: 'x_i.ptr' was declared here 2555 | Chars_holder x_i; | ^~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GetPools.c -o GetPools.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Import.c -o Import.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c InformationContent.c -o InformationContent.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IntDist.c -o IntDist.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ManipulateXStringSet.c -o ManipulateXStringSet.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:406:25: warning: 'ans' may be used uninitialized [-Wmaybe-uninitialized] 406 | SET_VECTOR_ELT(ret, s, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ MeltPolymer.c:53:19: note: 'ans' was declared here 53 | SEXP ret, ans; | ^~~ MeltPolymer.c:358:41: warning: 'rans' may be used uninitialized [-Wmaybe-uninitialized] 358 | *(rans + k + l*s) += 1; | ^~~~~~~~~~~~~~~~~ MeltPolymer.c:54:17: note: 'rans' was declared here 54 | double *rans; | ^~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MovingAverage.c -o MovingAverage.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NNLS.c -o NNLS.o NNLS.c: In function 'NNLS': NNLS.c:78:51: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 78 | *rPercentComplete = floor(100*((double)i + 1)/(double)l); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NNLS.c:40:34: note: 'rPercentComplete' was declared here 40 | int i, j, k, before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from E:/biocbuild/bbs-3.21-bioc/R/include/Rdefines.h:41, from NNLS.c:17: E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:927:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 927 | #define eval Rf_eval NNLS.c:82:41: note: in expansion of macro 'eval' 82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:48:14: note: 'percentComplete' was declared here 48 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:927:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 927 | #define eval Rf_eval NNLS.c:82:41: note: in expansion of macro 'eval' 82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:48:31: note: 'utilsPackage' was declared here 48 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Order.c -o Order.o Order.c: In function 'radixOrder': Order.c:169:41: warning: 'bounds' may be used uninitialized [-Wmaybe-uninitialized] 169 | #pragma omp parallel num_threads(NTHREADS) | ^~~ Order.c:99:19: note: 'bounds' was declared here 99 | R_xlen_t *bounds; | ^~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PairwiseAlignment.c -o PairwiseAlignment.o PairwiseAlignment.c: In function 'alignPair._omp_fn.0': PairwiseAlignment.c:446:39: warning: 'p3' may be used uninitialized [-Wmaybe-uninitialized] 446 | p3[0] = l1; | ~~~~~~^~~~ PairwiseAlignment.c:176:24: note: 'p3' was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:447:39: warning: 'p4' may be used uninitialized [-Wmaybe-uninitialized] 447 | p4[0] = l2 - j1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:176:29: note: 'p4' was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:450:39: warning: 'p1' may be used uninitialized [-Wmaybe-uninitialized] 450 | p1[0] = l2; | ~~~~~~^~~~ PairwiseAlignment.c:176:14: note: 'p1' was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:451:39: warning: 'p2' may be used uninitialized [-Wmaybe-uninitialized] 451 | p2[0] = l1 - i1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:176:19: note: 'p2' was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c: In function 'alignPairs': PairwiseAlignment.c:1108:17: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 1108 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1036:25: note: 'rPercentComplete' was declared here 1036 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ PairwiseAlignment.c:1108:17: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 1108 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1038:14: note: 'percentComplete' was declared here 1038 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ PairwiseAlignment.c:1108:17: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 1108 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1038:31: note: 'utilsPackage' was declared here 1038 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PopulationGenetics.c -o PopulationGenetics.o PopulationGenetics.c: In function 'correlationProfile': PopulationGenetics.c:136:51: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 136 | *rPercentComplete = floor(100*soFar/tot); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ PopulationGenetics.c:43:43: note: 'rPercentComplete' was declared here 43 | int i, j, k, p, I, J, v, before, *rPercentComplete; | ^~~~~~~~~~~~~~~~ PopulationGenetics.c:136:51: warning: 'tot' may be used uninitialized [-Wmaybe-uninitialized] 136 | *rPercentComplete = floor(100*soFar/tot); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ PopulationGenetics.c:44:31: note: 'tot' was declared here 44 | double weight, soFar, tot; | ^~~ In file included from E:/biocbuild/bbs-3.21-bioc/R/include/Rdefines.h:41, from PopulationGenetics.c:17: E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:927:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 927 | #define eval Rf_eval PopulationGenetics.c:139:41: note: in expansion of macro 'eval' 139 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ PopulationGenetics.c:53:14: note: 'percentComplete' was declared here 53 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:927:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 927 | #define eval Rf_eval PopulationGenetics.c:139:41: note: in expansion of macro 'eval' 139 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ PopulationGenetics.c:53:31: note: 'utilsPackage' was declared here 53 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictDBN.c -o PredictDBN.o PredictDBN.c: In function 'predictDBN': PredictDBN.c:598:25: warning: 'leftSymbol' may be used uninitialized [-Wmaybe-uninitialized] 598 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:486:14: note: 'leftSymbol' was declared here 486 | char leftSymbol, rightSymbol; | ^~~~~~~~~~ PredictDBN.c:598:25: warning: 'rightSymbol' may be used uninitialized [-Wmaybe-uninitialized] 598 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:486:26: note: 'rightSymbol' was declared here 486 | char leftSymbol, rightSymbol; | ^~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictHEC.c -o PredictHEC.o PredictHEC.c: In function 'predictHEC': PredictHEC.c:51:31: warning: 'rans' may be used uninitialized [-Wmaybe-uninitialized] 51 | double HEC[N], temp, *rans; | ^~~~ PredictHEC.c:247:43: warning: 'states' may be used uninitialized [-Wmaybe-uninitialized] 247 | states[j] = nms[0]; | ~~~~~~~~~~^~~~~~~~ PredictHEC.c:52:15: note: 'states' was declared here 52 | char *states; | ^~~~~~ PredictHEC.c:273:25: warning: 'ans' may be used uninitialized [-Wmaybe-uninitialized] 273 | SET_VECTOR_ELT(ret, i, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictHEC.c:59:19: note: 'ans' was declared here 59 | SEXP ret, ans; | ^~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_decipher.c -o R_init_decipher.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Search.c -o Search.o Search.c: In function 'searchIndex._omp_fn.0': Search.c:578:92: warning: 'subScores' may be used uninitialized [-Wmaybe-uninitialized] 578 | if (lkup != NA_INTEGER && subScores[p1*l_i.length + lkup] != NA_REAL) | ^ Search.c:317:33: note: 'subScores' was declared here 317 | double *subScores; // substitution scores (if maxIt > 0) | ^~~~~~~~~ Search.c:449:66: warning: 'score' may be used uninitialized [-Wmaybe-uninitialized] 449 | score2[j] = score[o1[j]]; | ^ Search.c:282:33: note: 'score' was declared here 282 | double *score, *addScore, *score2, *addScore2; | ^~~~~ Search.c:450:72: warning: 'addScore' may be used uninitialized [-Wmaybe-uninitialized] 450 | addScore2[j] = addScore[o1[j]]; | ^ Search.c:282:41: note: 'addScore' was declared here 282 | double *score, *addScore, *score2, *addScore2; | ^~~~~~~~ Search.c:587:83: warning: 'maxLen' may be used uninitialized [-Wmaybe-uninitialized] 587 | if (deltaTarget >= maxSep + maxLen) { | ~~~~~~~^~~~~~~~ Search.c:560:45: note: 'maxLen' was declared here 560 | int maxLen; // maximum observed length | ^~~~~~ Search.c:555:59: warning: 's_j.ptr' may be used uninitialized [-Wmaybe-uninitialized] 555 | Chars_holder p_i, s_j; | ^~~ Search.c:1150:72: warning: 'len' may be used uninitialized [-Wmaybe-uninitialized] 1150 | anchor[k++] = posQuery[p] + len[p] - 1; | ^ Search.c:370:30: note: 'len' was declared here 370 | int *len; // length of each hit | ^~~ Search.c:1139:58: warning: 'chain' may be used uninitialized [-Wmaybe-uninitialized] 1139 | while (p != chain[p]) { | ^ Search.c:369:30: note: 'chain' was declared here 369 | int *chain; // set of joined hits per match | ^~~~~ Search.c:371:30: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] 371 | int *res; // indices of results | ^~~ Search.c: In function 'searchIndex': Search.c:224:17: warning: 'sM' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:111:17: note: 'sM' was declared here 111 | double *sM, dS; | ^~ Search.c:224:17: warning: 'dS' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:111:21: note: 'dS' was declared here 111 | double *sM, dS; | ^~ Search.c:224:17: warning: 'lkup_row' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:112:14: note: 'lkup_row' was declared here 112 | int *lkup_row, *lkup_col, *pwv; | ^~~~~~~~ Search.c:224:17: warning: 'lkup_col' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:112:25: note: 'lkup_col' was declared here 112 | int *lkup_row, *lkup_col, *pwv; | ^~~~~~~~ Search.c:224:17: warning: 'pwv' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:112:36: note: 'pwv' was declared here 112 | int *lkup_row, *lkup_col, *pwv; | ^~~ Search.c:224:17: warning: 'scores' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:113:17: note: 'scores' was declared here 113 | double *scores, *addScores; | ^~~~~~ Search.c:224:17: warning: 'addScores' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:113:26: note: 'addScores' was declared here 113 | double *scores, *addScores; | ^~~~~~~~~ Search.c:224:17: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:174:25: note: 'rPercentComplete' was declared here 174 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ Search.c:224:17: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:176:14: note: 'percentComplete' was declared here 176 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Search.c:224:17: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:176:31: note: 'utilsPackage' was declared here 176 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ Search.c:224:17: warning: 'matrices' may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:217:16: note: 'matrices' was declared here 217 | int ***matrices; | ^~~~~~~~ Search.c:1287:38: warning: 'anchors' may be used uninitialized [-Wmaybe-uninitialized] 1287 | int *anchor = anchors[j]; | ^~~~~~ Search.c:1232:15: note: 'anchors' was declared here 1232 | int **anchors; // pointers to anchor positions | ^~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TerminalMismatch.c -o TerminalMismatch.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Translate.c -o Translate.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Utils.c -o Utils.o Utils.c: In function 'splitPartitions': Utils.c:990:35: warning: 'change' may be used uninitialized [-Wmaybe-uninitialized] 990 | } else if (change - j >= m && // large enough partition | ~~~~~~~^~~ Utils.c:984:13: note: 'change' was declared here 984 | int change; // index before start of partition | ^~~~~~ Utils.c: In function 'matchColumns': Utils.c:1198:55: warning: 'lkup' may be used uninitialized [-Wmaybe-uninitialized] 1198 | int val = lkup[(unsigned char)x_i.ptr[o[j]]]; | ^ Utils.c:1130:14: note: 'lkup' was declared here 1130 | int *lkup; | ^~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VectorSums.c -o VectorSums.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterME.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 PopulationGenetics.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 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs/x64 ** 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 ** 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 | 0.07 | 0.00 | 0.06 | |
Add2DB | 0.84 | 0.06 | 0.95 | |
AdjustAlignment | 0.23 | 0.00 | 0.25 | |
AlignDB | 1.36 | 0.10 | 1.48 | |
AlignPairs | 4.24 | 0.08 | 4.36 | |
AlignProfiles | 1.45 | 0.07 | 1.53 | |
AlignSeqs | 207.64 | 7.30 | 215.05 | |
AlignSynteny | 3.63 | 0.06 | 3.68 | |
AlignTranslation | 15.25 | 0.83 | 16.08 | |
AmplifyDNA | 0.02 | 0.00 | 0.03 | |
Array2Matrix | 8.70 | 0.06 | 8.77 | |
BLOSUM | 0.03 | 0.02 | 0.04 | |
BrowseDB | 0.06 | 0.00 | 0.06 | |
BrowseSeqs | 36.86 | 1.42 | 38.38 | |
CalculateEfficiencyArray | 0.02 | 0.02 | 0.03 | |
CalculateEfficiencyFISH | 0 | 0 | 0 | |
CalculateEfficiencyPCR | 0 | 0 | 0 | |
Clusterize | 7.01 | 0.25 | 7.28 | |
Codec | 1.47 | 0.00 | 1.47 | |
ConsensusSequence | 0.17 | 0.02 | 0.20 | |
Cophenetic | 4.15 | 0.07 | 4.20 | |
CorrectFrameshifts | 19.23 | 0.92 | 20.15 | |
CreateChimeras | 1.05 | 0.00 | 1.05 | |
DB2Seqs | 0.03 | 0.00 | 0.05 | |
DesignArray | 7.47 | 0.06 | 7.53 | |
DesignPrimers | 0.00 | 0.01 | 0.01 | |
DesignProbes | 0 | 0 | 0 | |
DesignSignatures | 0.03 | 0.00 | 0.03 | |
DetectRepeats | 15.61 | 0.61 | 16.24 | |
DigestDNA | 0.15 | 0.00 | 0.15 | |
Disambiguate | 0.05 | 0.00 | 0.05 | |
DistanceMatrix | 32.63 | 0.83 | 33.47 | |
ExtractGenes | 70.67 | 2.50 | 73.34 | |
FindChimeras | 0.08 | 0.01 | 0.10 | |
FindGenes | 70.90 | 2.82 | 73.82 | |
FindNonCoding | 72.77 | 11.65 | 84.63 | |
FindSynteny | 1.83 | 0.08 | 1.92 | |
FormGroups | 0.11 | 0.02 | 0.12 | |
Genes-class | 63.80 | 2.75 | 66.75 | |
HEC_MI | 0.20 | 0.04 | 0.25 | |
IdConsensus | 0.42 | 0.00 | 0.42 | |
IdLengths | 0.03 | 0.00 | 0.03 | |
IdTaxa | 10.41 | 0.68 | 11.07 | |
IdentifyByRank | 0.03 | 0.00 | 0.03 | |
IndexSeqs | 1.19 | 0.03 | 1.22 | |
InferRecombination | 26.53 | 0.64 | 27.17 | |
InvertedIndex-class | 0.75 | 0.01 | 0.76 | |
LearnNonCoding | 121.52 | 7.22 | 128.79 | |
LearnTaxa | 6.96 | 2.02 | 8.98 | |
MIQS | 0.04 | 0.04 | 0.11 | |
MMLSUM | 0.03 | 0.00 | 0.06 | |
MODELS | 0 | 0 | 0 | |
MapCharacters | 4.61 | 0.44 | 5.14 | |
MaskAlignment | 0.78 | 0.06 | 0.96 | |
MeltDNA | 0.09 | 0.00 | 0.11 | |
NNLS | 0 | 0 | 0 | |
NonCoding-class | 0.06 | 0.04 | 0.10 | |
NonCodingRNA | 0.14 | 0.00 | 0.18 | |
OrientNucleotides | 0.71 | 0.00 | 0.70 | |
PAM | 0.00 | 0.03 | 0.05 | |
PFASUM | 0.01 | 0.01 | 0.04 | |
PredictDBN | 0.02 | 0.00 | 0.02 | |
PredictHEC | 0.39 | 0.02 | 0.47 | |
RESTRICTION_ENZYMES | 0.00 | 0.01 | 0.06 | |
ReadDendrogram | 0.03 | 0.00 | 0.06 | |
RemoveGaps | 0.02 | 0.00 | 0.02 | |
ScoreAlignment | 5.67 | 0.32 | 5.98 | |
SearchDB | 0.08 | 0.00 | 0.08 | |
SearchIndex | 1.64 | 0.12 | 1.78 | |
Seqs2DB | 0.12 | 0.02 | 0.27 | |
StaggerAlignment | 14.19 | 1.58 | 15.76 | |
Synteny-class | 2.53 | 0.01 | 2.57 | |
Taxa-class | 11.28 | 0.47 | 11.76 | |
TerminalChar | 0.02 | 0.00 | 0.02 | |
TileSeqs | 4.62 | 0.02 | 4.64 | |
TrainingSet_16S | 2.38 | 0.12 | 2.50 | |
Treeline | 76.01 | 2.09 | 78.12 | |
TrimDNA | 0.17 | 0.00 | 0.19 | |
WriteDendrogram | 0.02 | 0.00 | 0.02 | |
WriteGenes | 62.16 | 3.52 | 65.90 | |
deltaGrules | 0.00 | 0.02 | 0.03 | |
deltaGrulesRNA | 0.03 | 0.00 | 0.05 | |
deltaHrules | 0.03 | 0.02 | 0.04 | |
deltaHrulesRNA | 0.00 | 0.03 | 0.03 | |
deltaSrules | 0.06 | 0.00 | 0.08 | |
deltaSrulesRNA | 0.03 | 0.00 | 0.03 | |