Hi,
I solved the error of decideTests() but now there is a whole bunch of
compilation error. Can anyone please guide me through this?
############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs
--no-resave-data groHMM
###
##############################################################################
##############################################################################
* checking for file �groHMM/DESCRIPTION� ... OK
* preparing �groHMM�:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package �groHMM� ...
** using staged installation
** libs
using C compiler: �gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0�
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include
-DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c AnnotateProbes.c -o
AnnotateProbes.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include
-DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c DecayAlgorithm.c -o
DecayAlgorithm.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include
-DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:43:
hmmHeader.h:301:16: warning: �expSum� defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: �MargainalizeSumLogProbOver� defined but not used
[-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include
-DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c RegisterRRoutines.c -o
RegisterRRoutines.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include
-DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c Windowing.c -o Windowing.o
Windowing.c: In function �WindowAnalysis�:
Windowing.c:146:13: warning: unused variable �II� [-Wunused-variable]
146 | int II = 0;
| ^~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include
-DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:50:
hmmHeader.h:301:16: warning: �expSum� defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: �MargainalizeSumLogProbOver� defined but not used
[-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36:
UsefulValues.h:39:15: warning: �VERY_LARGE_DOUBLE_VALUE� defined but not used
[-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include
-DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c hmmFwBw.c -o hmmFwBw.o
hmmFwBw.c: In function �forward�:
hmmFwBw.c:142:7: warning: this �for� clause does not guard...
[-Wmisleading-indentation]
142 | for(k=1; k<n; k++)
| ^~~
hmmFwBw.c:145:9: note: ...this statement, but the latter is misleadingly
indented as if it were guarded by the �for�
145 | for (k = 0; k<n; k++) {
| ^~~
In file included from hmmFwBw.c:45:
hmmHeader.h: At top level:
hmmHeader.h:301:16: warning: �expSum� defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: �MargainalizeSumLogProbOver� defined but not used
[-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36:
UsefulValues.h:39:15: warning: �VERY_LARGE_DOUBLE_VALUE� defined but not used
[-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include
-DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c hmmMiscFunctions.c -o
hmmMiscFunctions.o
hmmMiscFunctions.c: In function �SStatsGamma�:
hmmMiscFunctions.c:235:37: warning: format �%d� expects argument of type �int�,
but argument 2 has type �double� [-Wformat=]
235 | if(!(logPP <= epsilon)) Rprintf("[SSallocGamma] -- \
| ^~~~~~~~~~~~~~~~~~~~
236 | Assertion about to fail! logPP= %d\n", logPP);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~
| |
| double
hmmMiscFunctions.c: In function �UpdateGamma�:
hmmMiscFunctions.c:274:27: warning: implicit declaration of function �Calloc�;
did you mean �calloc�? [-Wimplicit-function-declaration]
274 | double *shape= (double*)Calloc(1, double);
| ^~~~~~
| calloc
hmmMiscFunctions.c:274:37: error: expected expression before �double�
274 | double *shape= (double*)Calloc(1, double);
| ^~~~~~
hmmMiscFunctions.c:275:37: error: expected expression before �double�
275 | double *scale= (double*)Calloc(1, double);
| ^~~~~~
hmmMiscFunctions.c:287:3: warning: implicit declaration of function �Free�; did
you mean �free�? [-Wimplicit-function-declaration]
287 | Free(shape);
| ^~~~
| free
hmmMiscFunctions.c: In function �SStatsNormExp�:
hmmMiscFunctions.c:384:10: warning: unused variable �wi� [-Wunused-variable]
384 | double wi, *newEx;
| ^~
hmmMiscFunctions.c: In function �UpdateNormExp�:
hmmMiscFunctions.c:417:10: warning: unused variable �epsilon�
[-Wunused-variable]
417 | double epsilon=0.00001;
| ^~~~~~~
In file included from hmmHeader.h:36,
from hmmMiscFunctions.c:43:
UsefulValues.h: At top level:
UsefulValues.h:39:15: warning: �VERY_LARGE_DOUBLE_VALUE� defined but not used
[-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195:
hmmMiscFunctions.o] Error 1
ERROR: compilation failed for package �groHMM�
* removing �/tmp/RtmpELy2EB/Rinst1165062fc12e4/groHMM�
-----------------------------------
ERROR: package installation failed
I haven't changed anything in the package.
Regards,
Tulip.
________________________________
From: James W. MacDonald <jmac...@uw.edu>
Sent: Tuesday, December 3, 2024 2:31 PM
To: Tulip Nandu <tulip.na...@utsouthwestern.edu>; Mike Smith
<grimbo...@gmail.com>
Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: RE: [Bioc-devel] groHMM package error
You need to commit your changes to g...@git.bioconductor.org, which you
apparently have not done as yet (you should have g...@git.bioconductor.org set
up as a remote which you can see by doing git remote -v). The last commit is
Jennifer Wokaty bumping the version for the last release:
/groHMM$ git log
commit a68457648cdef96ae2a8f40c484496e935d0fcb3 (HEAD -> devel, origin/master,
origin/devel, origin/HEAD)
Author: J Wokaty <jennifer.wok...@sph.cuny.edu>
Date: Tue Oct 29 09:56:11 2024 -0400
bump x.y.z version to odd y following creation of RELEASE_3_20 branch
You also need to bump the version number in order to get the new version to
build. You also need to make changes to the RELEASE_3_20 branch if you want the
fix to propagate to the release version of your package. Please see the git
version control section of the development pages
https://urldefense.com/v3/__https://contributions.bioconductor.org/git-version-control.html__;!!MznTZTSvDXGV0Co!D1Ec1At0koOWiqp-WDw8kmv5F2XS6u9FgDh9_6bOg6sahspYVpDQH4VMAWnhLzWraEuUptCNTFhuhD3a6ZVoPFJgJ1w$
-----Original Message-----
From: Bioc-devel <bioc-devel-boun...@r-project.org> On Behalf Of Tulip Nandu
Sent: Tuesday, December 3, 2024 3:14 PM
To: Mike Smith <grimbo...@gmail.com>
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] groHMM package error
Hi,
I edited the file based on Mike' s suggestion on the git page (image1) but
doesn't seem to reflect when I clone the file using the git clone bioconductor
package yet. Can someone confirm it will be done and nothing else I have to do
from my end.
Let me know.
Regards,
Tulip.
________________________________
From: Mike Smith <grimbo...@gmail.com>
Sent: Tuesday, November 26, 2024 2:50 AM
To: Tulip Nandu <tulip.na...@utsouthwestern.edu>
Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] groHMM package error
EXTERNAL MAIL
Dear Tulip,
The decideTestsDGE() function was deprecated in edgeR 4.2 and removed in the
new 4.4 release. You can find some notes ion this n the NEWS at
https://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS__;!!K-Hz7m0Vt54!ml36G27n5i71mmZqYh9kGx64fb8MnMWqcgTRb-IOUtzTvcuIr8z00917gwIae3eKB558z662Sqs-Iu35-pnRAO0wmBtwCQ$
<https://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS__;!!MznTZTSvDXGV0Co!BCGS40g3d3SSGednQhbxHgpWzGAsYc9EsCe70-JZ9IXVg3a8PO-zA19gV1ChkR4Rh_ekHivdYDmFEO8pn_DJEQx-jd1t$>
It looks to me like you should be able to use decideTests() as a drop in
replacement in your package.
Best,
Mike
On Mon, 25 Nov 2024 at 23:23, Tulip Nandu
<tulip.na...@utsouthwestern.edu<mailto:tulip.na...@utsouthwestern.edu>> wrote:
Hi,
I keep getting this message from Bioconductor for groHMM package and don't know
what the error is since I haven't changed anything in the package. Can someone
please help?
Regards,
Tulip.
"Warning in makeConsensusAnnotations(kgChr7, keytype = "gene_id", mc.cores =
getOption("mc.cores")) :
562 ranges do not have gene_id and they are
dropped
Reduce isoforms(701) ... OK
Truncate overlapped ranges ... OK
'select()' returned 1:1 mapping between keys and columns Calculate overlapping
... OK Scale overlapping ... OK
Warning: file stem
�/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpkfITSx/Rbuild130dca6dd2fd85/groHMM/vignettes/groHMM-fig2�
is not portable Calculate overlapping ... OK Scale overlapping ... OK Loading
required package: limma
Attaching package: �limma�
The following object is masked from �package:BiocGenerics�:
plotMA
Error: processing vignette 'groHMM.Rnw' failed with diagnostics:
chunk 21 (label = DE for trascripts)
Error in decideTestsDGE(et, p = 0.001, adjust = "fdr") :
could not find function "decideTestsDGE"
--- failed re-building �groHMM.Rnw�
SUMMARY: processing the following file failed:
�groHMM.Rnw�
Error: Vignette re-building failed.
Execution halted"
________________________________
UT Southwestern
Medical Center
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