Question

readCufflinks problem with extdata

4

Entering edit mode

biakemi ▴ 40

@biakemi-13355

Last seen 7.5 years ago

Hi,

I recently started working with RNA-Seq and I reached the step where I analyze my data using cummeRbund. I thought of doing some tutorials first to get to know the package, but I'm having problems with that.

I followed the instructions in the sample workflow:

source("https://bioconductor.org/biocLite.R")
biocLite("cummeRbund")
library(cummeRbund)

cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund"))

But when I run the readCufflinks command, the following errors appear:

Creating database /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/cuffData.db
Reading Run Info File /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/run.info
Writing runInfo Table
Reading Read Group Info /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/read_groups.info
Writing replicates Table
Reading /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cummeRbund/extdata/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

I thought it was weird, since it is a tutorial data, so the columns should have the correct name? Would this be an issue of installation? Any help is welcomed!

cummerbund • 11k views

ADD COMMENT • link updated 7.3 years ago by markus.ball ▴ 10 • written 7.5 years ago by biakemi ▴ 40

0

Entering edit mode

The same issue here:

R » dir = "../"
R » outdir = "BM_I_vs_SP_I"
R » cuff <- readCufflinks(dir = file.path(dir, outdir), rebuild = TRUE)
Creating database ..//BM_I_vs_SP_I/cuffData.db
Reading Run Info File ..//BM_I_vs_SP_I/run.info
Writing runInfo Table
Reading Read Group Info  ..//BM_I_vs_SP_I/read_groups.info
Writing replicates Table
Reading Var Model Info  ..//BM_I_vs_SP_I/var_model.info
Writing varModel Table
Reading ..//BM_I_vs_SP_I/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Erro: Column name mismatch.
Além disso: There were 50 or more warnings (use warnings() to see the first 50)

sessionInfo() is as follows:

R » sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=pt_BR.UTF-8       LC_NUMERIC=C               LC_TIME=pt_BR.UTF-8        LC_COLLATE=pt_BR.UTF-8    
 [5] LC_MONETARY=pt_BR.UTF-8    LC_MESSAGES=pt_BR.UTF-8    LC_PAPER=pt_BR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] cummeRbund_2.18.0    Gviz_1.20.0          rtracklayer_1.36.6   GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 
 [6] IRanges_2.10.5       S4Vectors_0.14.7     fastcluster_1.1.24   reshape2_1.4.3       ggplot2_2.2.1       
[11] RSQLite_2.0          BiocGenerics_0.22.1  BiocInstaller_1.26.1 setwidth_1.0-4       colorout_1.1-2      

loaded via a namespace (and not attached):
 [1] httr_1.3.1                    Biobase_2.36.2                AnnotationHub_2.8.3          
 [4] bit64_0.9-7                   splines_3.4.3                 shiny_1.0.5                  
 [7] Formula_1.2-2                 interactiveDisplayBase_1.14.0 latticeExtra_0.6-28          
[10] blob_1.1.0                    BSgenome_1.44.2               GenomeInfoDbData_0.99.0      
[13] Rsamtools_1.28.0              yaml_2.1.16                   pillar_1.1.0                 
[16] backports_1.1.2               lattice_0.20-35               biovizBase_1.24.0            
[19] digest_0.6.14                 RColorBrewer_1.1-2            XVector_0.16.0               
[22] checkmate_1.8.5               colorspace_1.3-2              httpuv_1.3.5                 
[25] htmltools_0.3.6               Matrix_1.2-12                 plyr_1.8.4                   
[28] pkgconfig_2.0.1               XML_3.98-1.9                  biomaRt_2.32.1               
[31] zlibbioc_1.22.0               xtable_1.8-2                  scales_0.5.0                 
[34] BiocParallel_1.10.1           htmlTable_1.11.2              tibble_1.4.2                 
[37] AnnotationFilter_1.0.0        SummarizedExperiment_1.6.5    GenomicFeatures_1.28.5       
[40] nnet_7.3-12                   lazyeval_0.2.1                mime_0.5                     
[43] survival_2.41-3               magrittr_1.5                  memoise_1.1.0                
[46] foreign_0.8-69                tools_3.4.3                   data.table_1.10.4-3          
[49] matrixStats_0.53.0            stringr_1.2.0                 munsell_0.4.3                
[52] cluster_2.0.6                 DelayedArray_0.2.7            ensembldb_2.0.4              
[55] AnnotationDbi_1.38.2          Biostrings_2.44.2             compiler_3.4.3               
[58] rlang_0.1.6                   RCurl_1.95-4.10               dichromat_2.0-0              
[61] rstudioapi_0.7                VariantAnnotation_1.22.3      htmlwidgets_1.0              
[64] bitops_1.0-6                  base64enc_0.1-3               gtable_0.2.0                 
[67] curl_3.1                      DBI_0.7                       R6_2.2.2                     
[70] GenomicAlignments_1.12.2      gridExtra_2.3                 knitr_1.18                   
[73] bit_1.1-12                    Hmisc_4.1-1                   ProtGenerics_1.8.0           
[76] stringi_1.1.6                 Rcpp_0.12.15                  rpart_4.1-12                 
[79] acepack_1.4.1

ADD REPLY • link 6.9 years ago Frederico Moraes Ferreira ▴ 100

score 4 · Answer 1 · 2017-07-08

4

Entering edit mode

Oskar ▴ 50

@oskar-13385

Last seen 5.8 years ago

Many thanks for all those answers. Here I copy and paste how I get this package working in R v. 3.3.3 (Windows users)

source("https://bioconductor.org/biocLite.R")
biocLite()

##### To install old version of packages:
install.packages("devtools")
require(devtools)

install_version("RSQLite", version = "1.1-2", repos = "http://cran.us.r-project.org")

biocLite("cummeRbund")
library(cummeRbund)

Here's my sessionInfo()

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] cummeRbund_2.16.0    Gviz_1.18.2          rtracklayer_1.34.2   GenomicRanges_1.26.4 GenomeInfoDb_1.10.3  IRanges_2.8.2       
 [7] S4Vectors_0.12.2     fastcluster_1.1.22   reshape2_1.4.2       ggplot2_2.2.1        RSQLite_1.1-2        BiocGenerics_0.20.0 
[13] devtools_1.13.2      BiocInstaller_1.24.0

ADD COMMENT • link 7.5 years ago Oskar ▴ 50

0

Entering edit mode

I'm having the same problem and when I use your fix I get the following error:

require(devtools)
Loading required package: devtools
Warning message:
package ‘devtools’ was built under R version 3.3.2
> install_version("RSQLite", version = "1.1-2", repos = "http://cran.us.r-project.org")
Downloading package from url: http://cran.us.r-project.org/src/contrib/Archive/RSQLite/RSQLite_1.1-2.tar.gz
Installation failed: Could not find build tools necessary to build RSQLite

I'm using a mac so it could be a compatibility issue, but any help would be greatly appreciated!

ADD REPLY • link 7.5 years ago jyoung • 0

0

Entering edit mode

You'll need to build RSQLite from source. For macOS, this requires XCode and compilers as described here.

ADD REPLY • link 7.5 years ago Martin Morgan 25k

0

Entering edit mode

I am having the same problem for quite a few days now, with no solution. As others stated, the cummeRbund does load a previous cuffdiff data but not the new one. I get the same error message as @biakemi. After updating R to 3.4.1 and trying @Oskar recommendation, I still get the same result.

Here is my sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=es_UY.UTF-8       LC_NUMERIC=C               LC_TIME=es_UY.UTF-8        LC_COLLATE=es_UY.UTF-8     LC_MONETARY=es_UY.UTF-8   
 [6] LC_MESSAGES=es_UY.UTF-8    LC_PAPER=es_UY.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_UY.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] cummeRbund_2.18.0    Gviz_1.20.0          rtracklayer_1.36.3   GenomicRanges_1.28.3 GenomeInfoDb_1.12.2  IRanges_2.10.2       S4Vectors_0.14.3    
 [8] fastcluster_1.1.22   reshape2_1.4.2       ggplot2_2.2.1        RSQLite_2.0          BiocGenerics_0.22.0  devtools_1.13.2

Anyone could solve this issue? Suggestions are welcomed!

ADD REPLY • link 7.5 years ago splepre • 0

0

Entering edit mode

From your sessionInfo(), RSQLite is too new; you're aiming for the version in Oskar's post.

ADD REPLY • link 7.5 years ago Martin Morgan 25k

0

Entering edit mode

Yes, you are correct. Now, I followed Oskar's post strictly, and I can't load cummeRbund package. I get the following error:

> library(cummeRbund)
Loading required package: Gviz
Error: package or namespace load failed for ‘Gviz’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace ‘RSQLite’ 1.1-2 is already loaded, but >= 2.0 is required
Error: package ‘Gviz’ could not be loaded
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=es_UY.UTF-8       LC_NUMERIC=C               LC_TIME=es_UY.UTF-8        LC_COLLATE=es_UY.UTF-8     LC_MONETARY=es_UY.UTF-8   
 [6] LC_MESSAGES=es_UY.UTF-8    LC_PAPER=es_UY.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_UY.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.26.0 RSQLite_2.0          devtools_1.13.2      rtracklayer_1.36.3   GenomicRanges_1.28.3 GenomeInfoDb_1.12.2  IRanges_2.10.2      
 [8] S4Vectors_0.14.3     fastcluster_1.1.22   reshape2_1.4.2       ggplot2_2.2.1        BiocGenerics_0.22.0

ADD REPLY • link 7.5 years ago splepre • 0

0

Entering edit mode

The basic problem is that cummeRbund needs to be updated for the recent RSQLite change.

The first solution is to wait for the maintainer to do this (they have been contacted). This requires patience.

The second solution is to basically 'make a mess' of your installation by downgrading packages to the version that works with the old version of RStudio. For GViz and other packages, you could use svn (http://bioconductor.org/developers/how-to/source-control/) or git / github(https://github.com/Bioconductor-mirror) to get the version before the maintainer updated their package. Generally, this will be tedious, require some skill / skill acquisition, and require patience.

ADD REPLY • link 7.5 years ago Martin Morgan 25k

0

Entering edit mode

Had the same problem but the aforementioned solution worked for me. Just to reciprocate the assemblage: (i) Windows 10, (ii) R version 3.3.3, and (iii) RSQLite version 1.1-2.

Thanks.

ADD REPLY • link 7.4 years ago Shaurya Jauhari • 0

0

Entering edit mode

This does not seem to work always. I kept getting error about `Gviz`, and `cummeRbund` not being compatible with `RSQLite` version `1.1-2`. It worked on my Laptop, but cannot get it to work on the cluster.

ADD REPLY • link 7.4 years ago Sameet Mehta ▴ 30

score 1 · Answer 2 · 2017-07-05

Also had this issue with the newest version of cummeRbund (installed on the newest version of R (3.4.1) with the newest version of Bioconductor). Definitely seems to be a bug somewhere.

The most recent version of this package that I was able to get this function working was acquired by manually installing RSQLite_1.1-2 from source and then using the previous build of Bioconductor (3.4) to install cummeRbund.

Here's my sessionInfo() that allows for a working function:

attached base packages: [1] grid stats4 parallel stats graphics grDevices utils [8] datasets methods base other attached packages: [1] cummeRbund_2.16.0 Gviz_1.18.2 rtracklayer_1.34.2 [4] GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 IRanges_2.8.2 [7] S4Vectors_0.12.2 fastcluster_1.1.22 reshape2_1.4.2 [10] ggplot2_2.2.1 RSQLite_1.1-2 BiocGenerics_0.20.0

score 1 · Answer 3 · 2017-07-06

1. Install R version: 3.3.2 from source

from https://cloud.r-project.org/

wget https://cloud.r-project.org/src/base/R-3/R-3.3.2.tar.gz

tar xf R-3.3.2.tar.gz

cd R-3.3.2

./configure

make

2. Install bioconductor 3.4

source("https://bioconductor.org/biocLite.R")

     biocLite()

3. Install RSQLite 1.1.2

install.packages("https://launchpad.net/ubuntu/+archive/primary/+files/r-cran-rsqlite_1.1-2.orig.tar.gz")

score 1 · Answer 4 · 2017-09-25

1

Entering edit mode

markus.ball ▴ 10

@markusball-14030

Last seen 7.3 years ago

So no solution yet?

ADD COMMENT • link 7.3 years ago markus.ball ▴ 10

score 0 · Answer 5 · 2017-07-03

Hi - I also have exactly the same issue. Not sure what is going on; but when I re-run an analysis (previously done with an old version) it turn out with the outcome posted by biakemi. Here is the output.

CuffSet instance with:

0 samples

0 genes

0 isoforms

0 TSS

0 CDS

0 promoters

0 splicing

0 relCDS

>

Any help will be appreciated.

score 0 · Answer 6 · 2017-07-05

0

Entering edit mode

ianmisner17 ▴ 20

@ianmisner17-7131

Last seen 7.5 years ago

United States

I'm having the exact same issue. Using the newest versions of R and Bioconductor. Seems to be a bug in the latest release of cummeRbund.

ADD COMMENT • link 7.5 years ago ianmisner17 ▴ 20

score 0 · Answer 7 · 2017-07-10

Very similar issue here. When trying to load cuffldiff output, my errors look like this:

Creating database /cuffData.db
Error in rsqlite_connect(dbname, loadable.extensions, flags, vfs) :
Could not connect to database:
unable to open database file

or

50+ of these:

1: In rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries

depending on how I submit it

The working directory is correct and I have formatted the input in as many ways as I can think of. I've re-run cuffdiff multiple times, still not working. Oddly, if I use cuffdiff output that was produced a year ago (using the same pipeline), it works.

I tried to get the package working by installing the other version on SQlite, but cummerbund will not proceed unless its updated.

I'm stuck. does anyone have a suggestion?

score 0 · Answer 8 · 2017-07-20

Hi, I have been facing the same problem which I have mentioned below.

cuff = readCufflinks(dbFile = "cuffData.db",
geneFPKM = "genes.fpkm_tracking",
geneDiff = "gene_exp.diff",
isoformFPKM = "isoforms.fpkm_tracking",
isoformDiff = "isoform_exp.diff",
TSSFPKM = "tss_groups.fpkm_tracking",
TSSDiff = "tss_group_exp.diff",
CDSFPKM = "cds.fpkm_tracking",
CDSExpDiff = "cds_exp.diff",
SplicingDiff = "splicing.diff",
CDSDiff = "CDS.diff",
PromotersDiff = "promoters.diff",
rebuild = T)

The output looks like:

Creating database C:/Users/Arpa.Samadder001/Desktop/new/cuffdiff/cuffData.db
Reading Run Info File C:/Users/Arpa.Samadder001/Desktop/new/cuffdiff/run.info
Writing runInfo Table
Reading Read Group Info C:/Users/Arpa.Samadder001/Desktop/new/cuffdiff/read_groups.info
Writing replicates Table
Reading Var Model Info C:/Users/Arpa.Samadder001/Desktop/new/cuffdiff/var_model.info
Writing varModel Table
Reading C:/Users/Arpa.Samadder001/Desktop/new/cuffdiff/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

I couldn't understand how to overcome this problem. Your help will be highly appreciated.

Thanks.

score 0 · Answer 9 · 2017-07-25

Dear all,

I followed all of the aforementioned recommendations but still face with the following error:

"Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)"

This error appeared when I updated my R and cummeRbund to the newest version. How can I solve this problem? Please help.
Kam

score 0 · Answer 10 · 2017-08-21

0

Entering edit mode

seungjoon.kim • 0

@seungjoonkim-13660

Last seen 7.4 years ago

Berlin

Hi I just installed cummeRbund and also have exactly the same issue with 50 or more warnings.

CuffSet instance with:

0 samples

0 genes

0 isoforms

0 TSS

0 CDS

0 promoters

0 splicing

0 relCDS

Seems not just my problems

ADD COMMENT • link 7.3 years ago seungjoon.kim • 0

0

Entering edit mode

I'm at the same point. I hope that this will get resolved through an update!

ADD REPLY • link 7.3 years ago brianagross • 0

0

Entering edit mode

Hello,

I have the same error. Do you have any updates ?

ADD REPLY • link 7.3 years ago shastry.a • 0

0

Entering edit mode

hey,

I have just received the same error. Were you guys able to solve the problem?

Efraim

ADD REPLY • link 7.1 years ago eculfa • 0

score 0 · Answer 11 · 2017-09-07

0

Entering edit mode

sdhutchins • 0

@sdhutchins-13910

Last seen 7.0 years ago

I'm having the same issue. I've installed RSQLite version 1.1-2, but now it seems GViz won't load because of the cummeRbund version.

Loading required package: Gviz
Error: package or namespace load failed for ‘Gviz’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace ‘RSQLite’ 1.1-2 is already loaded, but >= 2.0 is required
Error: package ‘Gviz’ could not be loaded

ADD COMMENT • link 7.3 years ago sdhutchins • 0

0

Entering edit mode

And after trying to download everything again, I get the following error:

Error in $<-.data.frame: replacement has 1 row, data has 0

ADD REPLY • link 7.3 years ago sdhutchins • 0