Erik Wright
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/DECIPHER |
| git_branch: RELEASE_3_16 |
| git_last_commit: 7de99ec |
| git_last_commit_date: 2022-11-01 11:06:21 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:02 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 487/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 2.26.0 (landing page) Erik Wright
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DECIPHER |
| Version: 2.26.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DECIPHER_2.26.0.tar.gz |
| StartedAt: 2023-04-10 20:08:55 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 20:41:55 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 1979.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DECIPHER.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DECIPHER_2.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DECIPHER.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.26.0’
* 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
* checking installed package size ... NOTE
installed size is 13.3Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 7.3Mb
extdata 2.3Mb
libs 1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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 106.584 0.232 106.818
MapCharacters 91.334 0.332 91.668
FindNonCoding 54.086 0.376 54.463
LearnNonCoding 49.823 3.986 54.364
BrowseSeqs 42.758 0.316 43.173
ExtractGenes 36.031 0.488 36.521
Genes-class 34.734 0.216 34.952
WriteGenes 34.156 0.096 34.252
FindGenes 31.414 0.184 31.599
AlignSeqs 21.619 0.367 21.987
CorrectFrameshifts 16.493 0.072 16.564
StaggerAlignment 11.408 0.084 11.493
AlignTranslation 11.211 0.152 11.365
Taxa-class 11.171 0.020 11.190
IdTaxa 10.603 0.040 10.643
DetectRepeats 10.047 0.111 10.159
TreeLine 7.601 0.052 7.652
LearnTaxa 6.805 0.828 7.633
Clusterize 5.218 0.056 5.274
* 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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
DECIPHER.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DECIPHER
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:424:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
424 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:61:39: note: ‘lGp’ was declared here
61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
| ^~~
AlignProfiles.c:426:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
426 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:61:44: note: ‘lGs’ was declared here
61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
| ^~~
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1266:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1266 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:808:39: note: ‘lGp’ was declared here
808 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c:1268:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1268 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:808:44: 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:378:11: 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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function ‘calculateHairpinDeltaG’:
CalculateDeltaG.c:375:26: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
375 | int i, j, k, count, s1, s2;
| ^~
CalculateDeltaG.c:375:22: warning: ‘s1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
375 | int i, j, k, count, s1, s2;
| ^~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces]
25 | double dH_DR[4][4] = {
| ^
26 | -11.5, -7.8, -7, -8.3,
| { }
27 | -10.4, -12.8, -16.3, -9.1,
| { }
28 | -8.6, -8, -9.3, -5.9,
| { }
29 | -7.8, -5.5, -9, -7.8
| {
30 | };
| }
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
31 | double dS_DR[4][4] = {
| ^
32 | -36.4, -21.6, -19.7, -23.9,
| { }
33 | -28.4, -31.9, -47.1, -23.5,
| { }
34 | -22.9, -17.1, -23.2, -12.3,
| { }
35 | -23.2, -13.5, -26.1, -21.9
| {
36 | };
| }
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
37 | double dH_DD[4][4] = {
| ^
38 | -7.9, -8.4, -7.8, -7.2,
| { }
39 | -8.5, -8, -10.6, -7.8,
| { }
40 | -8.2, -9.8, -8, -8.4,
| { }
41 | -7.2, -8.2, -8.5, -7.9
| {
42 | };
| }
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
43 | double dS_DD[4][4] = {
| ^
44 | -22.2, -22.4, -21, -20.4,
| { }
45 | -22.7, -19.9, -27.2, -21,
| { }
46 | -22.2, -24.4, -19.9, -22.4,
| { }
47 | -21.3, -22.2, -22.7, -22.2
| {
48 | };
| }
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
49 | double dH_RR[4][4] = {
| ^
50 | -6.6, -10.17, -7.65, -5.76,
| { }
51 | -10.56, -12.21, -7.95, -7.65,
| { }
52 | -13.37, -14.21, -12.21, -10.17,
| { }
53 | -8.11, -13.37, -10.56, -6.6
| {
54 | };
| }
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
55 | double dS_RR[4][4] = {
| ^
56 | -18.38, -26.03, -19.18, -15.67,
| { }
57 | -28.25, -30.02, -19.18, -19.18,
| { }
58 | -35.68, -34.85, -30.02, -26.03,
| { }
59 | -22.59, -35.68, -28.25, -18.38
| {
60 | };
| }
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:466:72: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
466 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
| ^~~
ChainSegments.c:466:67: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
466 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
| ^~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Cluster.c -o Cluster.o
Cluster.c: In function ‘cluster._omp_fn.0’:
Cluster.c:403:15: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
403 | minCs[i] = minC;
| ~~~~~~~~~^~~~~~
Cluster.c:231:50: 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:427:30: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
427 | minCols[rowIndices[i]] = minC;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:231:50: note: ‘minC’ was declared here
231 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c: In function ‘cluster’:
Cluster.c:231:50: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c:739:9: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized]
739 | nDiv[i] = nDiv[i + 1];
| ^
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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:6905:10: 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-3.16-bioc/R/include/Rdefines.h:38,
from ClusterML.c:11:
/home/biocbuild/bbs-3.16-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:6737:10: note: ‘I’ was declared here
6737 | double *I;
| ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/include/Rdefines.h:38,
from ClusterML.c:11:
/home/biocbuild/bbs-3.16-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:6736:7: note: ‘Up’ was declared here
6736 | int *Up;
| ^~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function ‘clusterMP._omp_fn.0’:
ClusterMP.c:72:15: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
72 | int i, j, k, m, w;
| ^
ClusterMP.c:125:9: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized]
125 | int *P;
| ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:540:3: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
540 | free(Up);
| ^~~~~~~~
ClusterMP.c:113:10: 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:113:10: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterMP.c:113:10: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CommonGaps.c -o CommonGaps.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:976:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
976 | p[c] = ((k - 1) >> 8) & 0xFF; // length of run
| ~~~^~~~
Compression.c:516:12: note: ‘k’ was declared here
516 | int i, j, k, pos;
| ^
Compression.c:1010:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1010 | count++;
| ~~~~~^~
Compression.c:542:29: note: ‘count’ was declared here
542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~~
Compression.c:1009:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1009 | word = (word << 8) | (unsigned int)reorder(byte);
| ~~~~~~^~~~~
Compression.c:542:23: note: ‘word’ was declared here
542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
Compression.c:1212:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1212 | p[c++] = rev==0 ? 254 : 255;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: ‘rev’ was declared here
543 | int lastTemp, currTemp, rev, len, len2, thresh = 1;
| ^~~
Compression.c:556:7: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
556 | int lower = 0;
| ^~~~~
Compression.c:1239:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1239 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
| ~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: ‘lastTriplet’ was declared here
629 | int run, lastTriplet, lastCase;
| ^~~~~~~~~~~
Compression.c:1325:4: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1325 | free(dict);
| ^~~~~~~~~~
Compression.c:542:17: note: ‘dict’ was declared here
542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfile’:
ConsensusSequence.c:1578:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1578 | double *DBN, *s;
| ^~~
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:456:14: warning: ‘length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
456 | } else if (length==2) { // run of length 3
| ^
ConsensusSequence.c:397:15: note: ‘length’ was declared here
397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
| ^~~~~~
ConsensusSequence.c:455:18: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
455 | *(runs + s) += weight;
| ^~
ConsensusSequence.c:397:23: note: ‘lastPos’ was declared here
397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
| ^~~~~~~
ConsensusSequence.c:1771:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1771 | double *HEC, *s;
| ^~~
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:2040:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2040 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:2040:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:1939:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1939 | int do_DBN, n, l, d;
| ^
ConsensusSequence.c:1938:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1938 | double *DBN, *s;
| ^~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2177:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2177 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:2177:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:2076:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2076 | int do_HEC, n, l, d;
| ^
ConsensusSequence.c:2075:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2075 | double *HEC, *s;
| ^~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
70 | double NN[4][4] = {
| ^
71 | -0.816507461,-2.5401714,-1.647430026,-1.184658548
| {
72 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
| }{
73 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
| }{
74 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
| }{
75 | };
| }
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
77 | double PM[4][4] = {
| ^
78 | -0.141370102,-0.439805276,-0.285236035,-0.205111781
| {
79 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
| }{
80 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
| }{
81 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
| }{
82 | };
| }
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
84 | double sMM[4][5][5][4] = {
| ^
85 | 0,0,0,0
| {{{
86 | ,1.545032445,1.254355018,1.491691514,1.329138183
| }{
87 | ,1.150635633,0.582415494,1.075877275,1.187937642
| }{
88 | ,1.203555051,1.001540513,0.864287715,0.717125848
| }{
89 | ,0.75,0.65,0.69,0.78
| }{
90 | ,0.630005348,0.18553379,0.730763505,0.709272397
| -
| }},{{
91 | ,0,0,0,0
| }{
92 | ,0.856582783,-0.143236405,0.716721488,0.603652831
| }{
93 | ,0.851622883,0.653168672,0.676545316,1.187937642
| }{
94 | ,0.75,0.65,0.69,0.78
| }{
95 | ,1.231861002,0.746214538,1.087821916,0.989140748
| -
| }},{{
96 | ,1.822113278,1.270687029,1.336192565,1.364584949
| }{
97 | ,0,0,0,0
| }{
98 | ,1.443665704,1.385046493,1.256013166,1.329138183
| }{
99 | ,0.75,0.65,0.69,0.78
| }{
100 | ,1.478009492,0.882097231,1.20450984,1.061002478
| -
| }},{{
101 | ,1.496720812,0.846496194,0.967868114,0.989140748
| }{
102 | ,0.766581547,-0.024857805,0.50754303,0.709272397
| }{
103 | ,0,0,0,0
| }{
104 | ,0.75,0.65,0.69,0.78
| }{
105 | ,0.75,0.65,0.69,0.78
| -
| }},{{
106 | ,0.75,0.65,0.69,0.78
| }{
107 | ,0.75,0.65,0.69,0.78
| }{
108 | ,0.76,0.65,0.69,0.78
| }{
109 | ,0,0,0,0
| }{
110 | ,0,0,0,0
| -
| }}},{{{
111 | ,1.295827995,0.84547091,0.91019099,1.256013166
| }{
112 | ,0.755889609,0.241428373,0.396379912,0.676545316
| }{
113 | ,0.99945386,0.740323132,0.435659206,0.864287715
| }{
114 | ,0.65,0.55,0.48,0.69
| }{
115 | ,0.843147406,0.101248351,0.49063599,0.50754303
| -
| }},{{
116 | ,0,0,0,0
| }{
117 | ,1.0651638,0.249934344,0.699352949,0.716721488
| }{
118 | ,0.871921533,0.59458138,0.396379912,1.075877275
| }{
119 | ,0.65,0.56,0.49,0.69
| }{
120 | ,1.07531714,0.318907854,0.653287717,0.967868114
| -
| }},{{
121 | ,1.099899195,0.730184613,0.661798984,1.336192565
| }{
122 | ,0,0,0,0
| }{
123 | ,1.45897431,1.318532145,0.91019099,1.491691514
| }{
124 | ,0.65,0.56,0.49,0.69
| }{
125 | ,1.242135174,0.894838095,1.108555445,1.20450984
| -
| }},{{
126 | ,0.911428974,0.524430101,0.653287717,1.087821916
| }{
127 | ,0.503209827,0.274849491,0.49063599,0.730763505
| }{
128 | ,0,0,0,0
| }{
129 | ,0.65,0.55,0.48,0.69
| }{
130 | ,0.65,0.55,0.48,0.69
| -
| }},{{
131 | ,0.65,0.56,0.49,0.69
| }{
132 | ,0.65,0.56,0.49,0.69
| }{
133 | ,0.65,0.55,0.48,0.69
| }{
134 | ,0,0,0,0
| }{
135 | ,0,0,0,0
| -
| }}},{{{
136 | ,1.100661785,0.969784756,1.318532145,1.385046493
| }{
137 | ,0.565895968,-0.060347902,0.59458138,0.653168672
| }{
138 | ,0.782168488,0.788161238,0.740323132,1.001540513
| }{
139 | ,0.68,0.46,0.55,0.65
| }{
140 | ,0.468913405,-0.469855984,0.274849491,-0.024857805
| -
| }},{{
141 | ,0,0,0,0
| }{
142 | ,0.258195131,-0.70438632,0.249934344,-0.143236405
| }{
143 | ,0.502914193,-0.060347902,0.241428373,0.582415494
| }{
144 | ,0.68,0.47,0.56,0.65
| }{
145 | ,0.584083861,0.258975454,0.524430101,0.846496194
| -
| }},{{
146 | ,0.968040559,0.797499702,0.730184613,1.270687029
| }{
147 | ,0,0,0,0
| }{
148 | ,1.081040749,0.969784756,0.84547091,1.254355018
| }{
149 | ,0.68,0.47,0.56,0.65
| }{
150 | ,1.048553951,0.728354541,0.894838095,0.882097231
| -
| }},{{
151 | ,0.88611252,0.258975454,0.318907854,0.746214538
| }{
152 | ,0.239520858,-0.469855984,0.101248351,0.18553379
| }{
153 | ,0,0,0,0
| }{
154 | ,0.68,0.46,0.55,0.65
| }{
155 | ,0.68,0.46,0.55,0.65
| -
| }},{{
156 | ,0.68,0.47,0.56,0.65
| }{
157 | ,0.68,0.47,0.56,0.65
| }{
158 | ,0.68,0.46,0.55,0.65
| }{
159 | ,0,0,0,0
| }{
160 | ,0,0,0,0
| -
| }}},{{{
161 | ,1.566899704,1.081040749,1.45897431,1.443665704
| }{
162 | ,0.976725675,0.502914193,0.871921533,0.851622883
| }{
163 | ,1.482046826,0.782168488,0.99945386,1.203555051
| }{
164 | ,0.85,0.68,0.65,0.76
| }{
165 | ,0.798628781,0.239520858,0.503209827,0.766581547
| -
| }},{{
166 | ,0,0,0,0
| }{
167 | ,1.141098246,0.258195131,1.0651638,0.856582783
| }{
168 | ,0.976725675,0.565895968,0.755889609,1.150635633
| }{
169 | ,0.85,0.68,0.65,0.75
| }{
170 | ,1.125403302,0.88611252,0.911428974,1.496720812
| -
| }},{{
171 | ,1.68169282,0.968040559,1.099899195,1.822113278
| }{
172 | ,0,0,0,0
| }{
173 | ,1.566899704,1.100661785,1.295827995,1.545032445
| }{
174 | ,0.85,0.68,0.65,0.75
| }{
175 | ,1.35948517,1.048553951,1.242135174,1.478009492
| -
| }},{{
176 | ,1.125403302,0.584083861,1.07531714,1.231861002
| }{
177 | ,0.798628781,0.468913405,0.843147406,0.630005348
| }{
178 | ,0,0,0,0
| }{
179 | ,0.85,0.68,0.65,0.75
| }{
180 | ,0.85,0.68,0.65,0.75
| -
| }},{{
181 | ,0.85,0.68,0.65,0.75
| }{
182 | ,0.85,0.68,0.65,0.75
| }{
183 | ,0.85,0.68,0.65,0.75
| }{
184 | ,0,0,0,0
| }{
185 | };
| }}}
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:834:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
834 | cycles += lastCycle - thisCycle;
| ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:37: note: ‘lastCycle’ was declared here
267 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
DesignProbes.c:834:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
834 | cycles += lastCycle - thisCycle;
| ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:48: note: ‘thisCycle’ was declared here
267 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:756:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
756 | if (!ci)
| ^~
DistanceMatrix.c:759:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
759 | while (i < ex) {
| ^~~~~
DistanceMatrix.c:778:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
778 | if (!cj)
| ^~
DistanceMatrix.c:781:4: 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:995:17: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized]
995 | (double)(OV + g)/(double)w1 < coverage &&
| ~~~~^~~~
DistanceMatrix.c:843:38: 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:843:34: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized]
843 | int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r;
| ^~
DistanceMatrix.c:1000:9: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1000 | if (o == 1) {
| ^
DistanceMatrix.c:843:53: 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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:315:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
315 | x = x + (x >> 4) & 0xF0F0F0F;
| ~~^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:381:14: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
381 | } else if (k==2) {
| ^
FindFrameshifts.c:318:19: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
318 | if (C[k*rc + j*r + i] >= 0) {
| ~^~
FindFrameshifts.c:320:13: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
320 | pos = i*3 + k + 1;
| ~^~
In file included from /home/biocbuild/bbs-3.16-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.16-bioc/R/include/Rinternals.h:895:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
895 | #define eval Rf_eval
| ^~~~~~~
FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.16-bioc/R/include/Rinternals.h:895:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
895 | #define eval Rf_eval
| ^~~~~~~
FindFrameshifts.c:162:7: note: ‘percentComplete’ was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
FindFrameshifts.c:468:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
468 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function ‘scoreCodonModel’:
GeneFinding.c:388:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
388 | Chars_holder x_i;
| ^~~
GeneFinding.c:432:29: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
432 | score += codons[lastVal*64 + val];
| ~~~~~~~^~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:791:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
791 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:892:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
892 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:973:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
973 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1059:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1059 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1131:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1131 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1216:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1216 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1286:21: 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:1252:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1252 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1379:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1379 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1496:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1496 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘couplingModel’:
GeneFinding.c:1598:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1598 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreCouplingModel’:
GeneFinding.c:1681:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1681 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1788:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1788 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1882:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1882 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1990:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1990 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
| ^
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:2090:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2090 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
| ^
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2276:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2276 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2419:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2419 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2520:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2520 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2578:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2578 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c InsertGaps.c -o InsertGaps.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces]
79 | double dH[4][4] = {
| ^
80 | -7.9,-8.4,-7.8,-7.2
| {
81 | ,-8.5,-8.0,-10.6,-7.8
| }{
82 | ,-8.2,-9.8,-8.0,-8.4
| }{
83 | ,-7.2,-8.2,-8.5,-7.9
| }{
84 | };
| }
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
88 | double dS[4][4] = {
| ^
89 | -22.2,-22.4,-21.0,-20.4
| {
90 | ,-22.7,-19.9,-27.2,-21.0
| }{
91 | ,-22.2,-24.4,-19.9,-22.4
| }{
92 | ,-21.3,-22.2,-22.7,-22.2
| }{
93 | };
| }
MeltPolymer.c:54:10: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
54 | double *rans;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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:871:21: 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:1033:10: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1033 | two != one) {
| ~~~~^~~~~~
MultiMatch.c:1008:7: note: ‘one’ was declared here
1008 | int one, two;
| ^~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/include/Rdefines.h:41,
from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.16-bioc/R/include/Rinternals.h:895:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
895 | #define eval Rf_eval
| ^~~~~~~
MultiMatch.c:247:24: note: ‘utilsPackage’ was declared here
247 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/include/Rdefines.h:41,
from MultiMatch.c:11:
/home/biocbuild/bbs-3.16-bioc/R/include/Rinternals.h:895:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
895 | #define eval Rf_eval
| ^~~~~~~
MultiMatch.c:247:7: note: ‘percentComplete’ was declared here
247 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
MultiMatch.c:330:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
330 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c NNLS.c -o NNLS.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’:
PairwiseAlignment.c:469:11: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
469 | P2[i] = p2;
| ~~~~~~^~~~
PairwiseAlignment.c:173:12: note: ‘p2’ was declared here
173 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:468:11: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
468 | P1[i] = p1;
| ~~~~~~^~~~
PairwiseAlignment.c:173:7: note: ‘p1’ was declared here
173 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:473:11: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
473 | P4[i] = p4;
| ~~~~~~^~~~
PairwiseAlignment.c:173:22: note: ‘p4’ was declared here
173 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:472:11: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
472 | P3[i] = p3;
| ~~~~~~^~~~
PairwiseAlignment.c:173:17: note: ‘p3’ was declared here
173 | int *p1, *p2, *p3, *p4;
| ^~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:869:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
869 | range2[0] = nucs[pos[prev]];// + 1;
| ^
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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:255:4: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
255 | SET_VECTOR_ELT(ret, i, ans);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:42:8: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
42 | char *states;
| ^~~~~~
PredictHEC.c:41:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
41 | double H, E, C, sum, *rans;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RemoveGaps.c -o RemoveGaps.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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:117:4: warning: ‘b’ may be used uninitialized in this function [-Wmaybe-uninitialized]
117 | free(b);
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/bbs-3.16-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-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-DECIPHER/00new/DECIPHER/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)
DECIPHER.Rcheck/DECIPHER-Ex.timings
| name | user | system | elapsed | |
| AA_REDUCED | 0.049 | 0.008 | 0.057 | |
| Add2DB | 0.259 | 0.012 | 0.272 | |
| AdjustAlignment | 0.191 | 0.000 | 0.191 | |
| AlignDB | 1.019 | 0.060 | 1.081 | |
| AlignProfiles | 0.795 | 0.012 | 0.808 | |
| AlignSeqs | 21.619 | 0.367 | 21.987 | |
| AlignSynteny | 2.441 | 0.024 | 2.466 | |
| AlignTranslation | 11.211 | 0.152 | 11.365 | |
| AmplifyDNA | 0.003 | 0.000 | 0.003 | |
| Array2Matrix | 4.347 | 0.044 | 4.392 | |
| BrowseDB | 0.021 | 0.000 | 0.020 | |
| BrowseSeqs | 42.758 | 0.316 | 43.173 | |
| CalculateEfficiencyArray | 0.016 | 0.000 | 0.016 | |
| CalculateEfficiencyFISH | 0.004 | 0.000 | 0.004 | |
| CalculateEfficiencyPCR | 0.004 | 0.000 | 0.004 | |
| Clusterize | 5.218 | 0.056 | 5.274 | |
| Codec | 1.348 | 0.000 | 1.348 | |
| ConsensusSequence | 0.152 | 0.008 | 0.160 | |
| Cophenetic | 0.178 | 0.000 | 0.178 | |
| CorrectFrameshifts | 16.493 | 0.072 | 16.564 | |
| CreateChimeras | 0.734 | 0.004 | 0.738 | |
| DB2Seqs | 0.015 | 0.003 | 0.018 | |
| DesignArray | 4.115 | 0.012 | 4.127 | |
| DesignPrimers | 0.000 | 0.000 | 0.001 | |
| DesignProbes | 0 | 0 | 0 | |
| DesignSignatures | 0.001 | 0.001 | 0.000 | |
| DetectRepeats | 10.047 | 0.111 | 10.159 | |
| DigestDNA | 0.143 | 0.000 | 0.143 | |
| Disambiguate | 0.044 | 0.000 | 0.044 | |
| DistanceMatrix | 0.032 | 0.000 | 0.032 | |
| ExtractGenes | 36.031 | 0.488 | 36.521 | |
| FindChimeras | 0.068 | 0.000 | 0.068 | |
| FindGenes | 31.414 | 0.184 | 31.599 | |
| FindNonCoding | 54.086 | 0.376 | 54.463 | |
| FindSynteny | 1.243 | 0.004 | 1.248 | |
| FormGroups | 0.034 | 0.004 | 0.038 | |
| Genes-class | 34.734 | 0.216 | 34.952 | |
| HEC_MI | 0.282 | 0.000 | 0.283 | |
| IdConsensus | 0.727 | 0.024 | 0.751 | |
| IdLengths | 0.018 | 0.000 | 0.017 | |
| IdTaxa | 10.603 | 0.040 | 10.643 | |
| IdentifyByRank | 0.020 | 0.001 | 0.021 | |
| LearnNonCoding | 49.823 | 3.986 | 54.364 | |
| LearnTaxa | 6.805 | 0.828 | 7.633 | |
| MIQS | 0.061 | 0.004 | 0.066 | |
| MODELS | 0.002 | 0.000 | 0.002 | |
| MapCharacters | 91.334 | 0.332 | 91.668 | |
| MaskAlignment | 0.426 | 0.012 | 0.438 | |
| MeltDNA | 0.039 | 0.000 | 0.040 | |
| NNLS | 0.003 | 0.000 | 0.003 | |
| NonCoding-class | 0.052 | 0.004 | 0.056 | |
| NonCodingRNA | 0.108 | 0.003 | 0.110 | |
| OrientNucleotides | 0.837 | 0.000 | 0.837 | |
| PFASUM | 0.024 | 0.004 | 0.029 | |
| PredictDBN | 106.584 | 0.232 | 106.818 | |
| PredictHEC | 0.245 | 0.004 | 0.249 | |
| RESTRICTION_ENZYMES | 0.000 | 0.002 | 0.003 | |
| ReadDendrogram | 0.057 | 0.001 | 0.058 | |
| RemoveGaps | 0.009 | 0.003 | 0.013 | |
| ScoreAlignment | 4.741 | 0.024 | 4.766 | |
| SearchDB | 0.03 | 0.00 | 0.03 | |
| Seqs2DB | 0.082 | 0.000 | 0.082 | |
| StaggerAlignment | 11.408 | 0.084 | 11.493 | |
| Synteny-class | 1.755 | 0.000 | 1.755 | |
| Taxa-class | 11.171 | 0.020 | 11.190 | |
| TerminalChar | 0.009 | 0.004 | 0.013 | |
| TileSeqs | 3.858 | 0.000 | 3.858 | |
| TrainingSet_16S | 1.778 | 0.016 | 1.794 | |
| TreeLine | 7.601 | 0.052 | 7.652 | |
| TrimDNA | 0.106 | 0.000 | 0.106 | |
| WriteDendrogram | 0.004 | 0.000 | 0.004 | |
| WriteGenes | 34.156 | 0.096 | 34.252 | |
| deltaGrules | 0.01 | 0.00 | 0.01 | |
| deltaHrules | 0.015 | 0.004 | 0.019 | |
| deltaHrulesRNA | 0.015 | 0.004 | 0.019 | |
| deltaSrules | 0.059 | 0.000 | 0.059 | |
| deltaSrulesRNA | 0.013 | 0.004 | 0.017 | |