installation error: collect2.exe: error: ld returned 1 exit status, no DLL was created

[Ci-TJ]

@Vivianstats Hi! I want to install the AIDE in R-3.6.3 on win10, but I get following error:

> library(GenomeInfoDb)
> library(IRanges)
> library(S4Vectors)
> library(GenomicRanges)
> library(Rsamtools)
> library(GenomicFeatures)
> library(Biostrings)
> library(GenomicAlignments)
> library(devtools)
> 
> devtools::install_github("Vivianstats/AIDE")
Downloading GitHub repo Vivianstats/AIDE@master
Skipping 8 packages not available: Biostrings, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, S4Vectors, GenomicRanges, Rsamtools
√  checking for file 'C:\Users\Ci\AppData\Local\Temp\RtmpA5gHRz\remotes3148fc16c94\Vivianstats-AIDE-beff824/DESCRIPTION'
-  preparing 'AIDE':
√  checking DESCRIPTION meta-information ... 
-  cleaning src
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'AIDE_1.0.0.tar.gz'

* installing *source* package 'AIDE' ...
** using staged installation
** libs

*** arch - i386
C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11  -I"E:/Study tools/R-3.6.3/include" -DNDEBUG  -I"E:/Study tools/R-3.6.3/library/Rcpp/include" -I"E:/Study tools/R-3.6.3/library/RcppArmadillo/include"        -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11  -I"E:/Study tools/R-3.6.3/include" -DNDEBUG  -I"E:/Study tools/R-3.6.3/library/Rcpp/include" -I"E:/Study tools/R-3.6.3/library/RcppArmadillo/include"        -O2 -Wall  -mtune=core2 -c calculate_h_supp.cpp -o calculate_h_supp.o
C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11  -I"E:/Study tools/R-3.6.3/include" -DNDEBUG  -I"E:/Study tools/R-3.6.3/library/Rcpp/include" -I"E:/Study tools/R-3.6.3/library/RcppArmadillo/include"        -O2 -Wall  -mtune=core2 -c estimation.cpp -o estimation.o
C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AIDE.dll tmp.def RcppExports.o calculate_h_supp.o estimation.o -LE:/Study tools/R-3.6.3/bin/i386 -lR
estimation.o:estimation.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE]+0x12d): undefined reference to `dgemv_'
estimation.o:estimation.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE]+0x2d7): undefined reference to `dgemv_'
estimation.o:estimation.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE]+0x5b8): undefined reference to `dgemv_'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'AIDE'
* removing 'E:/Study tools/R-3.6.3/library/AIDE'
Error: Failed to install 'AIDE' from GitHub:
  (converted from warning) installation of package ‘C:/Users/Ci/AppData/Local/Temp/RtmpA5gHRz/file31484ae4e0d/AIDE_1.0.0.tar.gz’ had non-zero exit status
> devtools::install_local("local_package/AIDE-master.zip")
Skipping 8 packages not available: Biostrings, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, S4Vectors, GenomicRanges, Rsamtools
* installing *source* package 'AIDE' ...
** using staged installation
** libs

*** arch - i386
C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11  -I"E:/Study tools/R-3.6.3/include" -DNDEBUG  -I"E:/Study tools/R-3.6.3/library/Rcpp/include" -I"E:/Study tools/R-3.6.3/library/RcppArmadillo/include"        -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11  -I"E:/Study tools/R-3.6.3/include" -DNDEBUG  -I"E:/Study tools/R-3.6.3/library/Rcpp/include" -I"E:/Study tools/R-3.6.3/library/RcppArmadillo/include"        -O2 -Wall  -mtune=core2 -c calculate_h_supp.cpp -o calculate_h_supp.o
C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11  -I"E:/Study tools/R-3.6.3/include" -DNDEBUG  -I"E:/Study tools/R-3.6.3/library/Rcpp/include" -I"E:/Study tools/R-3.6.3/library/RcppArmadillo/include"        -O2 -Wall  -mtune=core2 -c estimation.cpp -o estimation.o
C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AIDE.dll tmp.def RcppExports.o calculate_h_supp.o estimation.o -LE:/Study tools/R-3.6.3/bin/i386 -lR
estimation.o:estimation.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE]+0x12d): undefined reference to `dgemv_'
estimation.o:estimation.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE]+0x2d7): undefined reference to `dgemv_'
estimation.o:estimation.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE]+0x5b8): undefined reference to `dgemv_'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'AIDE'
* removing 'E:/Study tools/R-3.6.3/library/AIDE'
Error: Failed to install 'AIDE-master.zip' from local:
  (converted from warning) installation of package ‘C:/Users/Ci/AppData/Local/Temp/RtmpA5gHRz/remotes314818e039e2/AIDE-master’ had non-zero exit status

How do I deal with it ? Best, Ci

[Vivianstats]

Hello Ci, It looks like the the error is because it fails to install the Bioconductor packages:

Biostrings, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, S4Vectors, GenomicRanges, Rsamtools

You can try to manually install these packages from Bioconductor first, and try installing AIDE again.

If possible, I also suggest that you talk to the server's administrator and see if they can help you install the package on the server.

Best, Vivian

[Ci-TJ]

Hi Vivian，

I have installed all the Bicoonductor packages successfully by BiocManager, and you can see I 'library' all the packages in R-3.6.3 on win10. Can AIDE be installed in win10 ? I also want to install AIDE on the server, but it's a sad story. Have you ever tried to install the AIDE in windows?

Best, Ci

[Vivianstats]

Hello Ci, Thanks for the report. I tested the installation on Mac and Linux, but not on Windows. It just came up to me that Windows does not support the parallel package in R, which is used to perform parallel computation for AIDE. Therefore, it may not be the best idea to run AIDE on windows. I'm sorry about the inconvenience. Is there any other platform that you might be able to use?

[Ci-TJ]

Hi， Vivian, It's a long story for me to install AIDE in my friend's servers, I get it.

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘AIDE’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c calculate_h_supp.cpp -o calculate_h_supp.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c estimation.cpp -o estimation.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o AIDE.so RcppExports.o calculate_h_supp.o estimation.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-AIDE/00new/AIDE/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (AIDE)
> library(aide)
Error in library(aide) : there is no package called ‘aide’
> library(AIDE)
>

it means that AIDE would never be able to install on window. That's will be a bad info.

Thanks, Ci

[Vivianstats]

Glad to know that you finally managed to install the package!

Since isoform identification needs read alignment and other preprocessing steps, we were assuming that users have access to computing servers or clusters when we developed the AIDE package. That's why we prioritized for the linux environment. If there's increasing need for the windows OS, we might update the package in the future.

[Ci-TJ]

@Vivianstats Sorry for bothering you agian. I used AIDE to process sorted bam files which reads alignments were processed by HISAT2. But the process has lasted nearly two days, I didn't find any outputs as you described.

 [ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$ cd ..
 [ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630]$ cd out_AIDE
[ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$ cat ../sorted_bamFile/index_samtools.sh
for line in $(cat ../Run_GSE66630)
do
        samtools index $line"_sorted.bam" $line"_sorted.bai"
done
[ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$ ll ../sorted_bamFile/ | head
total 237939068
drwxrwxr-x  2 ymwang ymwang       8192 Apr 23 21:29 ./
drwxrwxr-x 17 ymwang ymwang       4096 Apr 23 22:33 ../
-rw-rw-r--  1 ymwang ymwang         97 Apr 23 18:57 index_samtools.sh
-rw-------  1 ymwang ymwang          0 Apr 23 19:43 nohup.out
-rw-rw-r--  1 ymwang ymwang    2411032 Apr 23 19:45 SRR1852470_sorted.bai
-rw-rw-r--  1 ymwang ymwang 3106056397 Apr 23 19:17 SRR1852470_sorted.bam
-rw-rw-r--  1 ymwang ymwang    2444408 Apr 23 19:46 SRR1852471_sorted.bai
-rw-rw-r--  1 ymwang ymwang 3520405065 Apr 23 19:17 SRR1852471_sorted.bam
-rw-rw-r--  1 ymwang ymwang    2482512 Apr 23 19:48 SRR1852472_sorted.bai
 [ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$ cat aide_GSE66630.R
# Using the AIDE for analyzing GSE66630

library(AIDE)
bamDir<-"/home2/ymwang/linqin/RNA-seq/Analysis/GSE66630/sorted_bamFile/"
temp<-list.files(path=bamDir,pattern="*.bam")

#for cycle
for ( i in 1:length(temp)){aide("/home2/ymwang/linqin/RNA-seq/AnnotGenome/release99/Mus_musculus.GRCm38.99.gtf",paste(bamDir,temp[i],sep=""),"/home2/ymwang/linqin/RNA-seq/refGenome/release99/Mus_musculus.GRCm38.dna.primary_assembly.fa","/home2/ymwang/linqin/RNA-seq/Analysis/GSE66630/out_AIDE",readLen=50,strandmode =0,ne=25, gene_model_path=NULL, flag=0)}

 [ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$nohup Rscript aide_GSE66630.R &
[ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$ ll
total 136
drwxrwxr-x  2 ymwang ymwang     56 Apr 23 22:32 ./
drwxrwxr-x 17 ymwang ymwang   4096 Apr 23 22:33 ../
-rw-rw-r--  1 ymwang ymwang    544 Apr 23 22:30 aide_GSE66630.R
-rw-------  1 ymwang ymwang 128210 Apr 25 12:23 nohup.out

 [ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$ tail nohup.out
[1] "gene: 8501"
[1] "gene: 6220"
[1] "gene: 6225"
[1] "gene: 6230"
[1] "gene: 8506"
[1] "gene: 6235"
[1] "gene: 6240"
[1] "gene: 8511"
[1] "gene: 6245"
[1] "gene: 8516"
 [ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$
[ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$ ll ../out_AIDEtemporary/
total 6564
drwxrwxr-x  3 ymwang ymwang      53 Apr 23 23:41 ./
drwxrwxr-x 17 ymwang ymwang    4096 Apr 23 22:33 ../
drwxrwxr-x  2 ymwang ymwang  172032 Apr 25 12:15 data/
-rw-rw-r--  1 ymwang ymwang 6459296 Apr 23 23:41 gene_models.RData

 [ymwang @ ~/linqin/RNA-seq/Analysis/GSE66630/out_AIDE]$ ll ../out_AIDEtemporary/data/ | head
total 28292
drwxrwxr-x 2 ymwang ymwang 172032 Apr 25 12:15 ./
drwxrwxr-x 3 ymwang ymwang     53 Apr 23 23:41 ../
-rw-rw-r-- 1 ymwang ymwang    384 Apr 24 13:11 1000.RData
-rw-rw-r-- 1 ymwang ymwang    353 Apr 24 12:25 1001.RData
-rw-rw-r-- 1 ymwang ymwang    276 Apr 24 13:27 1002.RData
-rw-rw-r-- 1 ymwang ymwang    305 Apr 24 13:41 1003.RData
-rw-rw-r-- 1 ymwang ymwang    305 Apr 24 13:02 1004.RData
-rw-rw-r-- 1 ymwang ymwang    325 Apr 24 13:12 1005.RData
-rw-rw-r-- 1 ymwang ymwang     70 Apr 24 12:25 1006.RData

Is it anything wrong with my processes? By the way, could you provide a detail example for me? Best, Ci

[Vivianstats]

The RData files in your output folder suggests that the function was generating the intermediate results and the computation was completed for around 8000 genes. However, I would expect the process to be done within 6 hours if you use around 8 cores. Otherwise, it will take longer. You can also consider using the ''genes" parameter to only compute abundances for a subset of genes if there's a gene list of interest.

[Ci-TJ]

Thanks for your reply. If my command is not wrong, I will waiting for output GTF files, although process have lasted for 3 days. I just used the default cores for computation, and I didn't know it will take so long. Another long story is beginning. I want to find some novel differential transcripts, so I may not consider using the "genes" parameter. Best, Ci