problem loading lumi package, Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
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lucashusquin ▴ 10
@lucashusquin-6959
Last seen 7.9 years ago
France

Hi All,

My name is Lucas, I'm currently doing an internship for my Master degree using Bioconductor to analyse the outcome of the HumanMethylation450 BeadChip on my cohort. I'm running ubuntu 14.04 LTS.

> sessionInfo()

R version 3.0.2

Platform: x86_64-pc-linux-gnu (64-bit)

Since yesterday (when I realized the issue, but it could have started earlier than that) I have not been able to load the lumi package. I had been using it for the past month and a half without any problems, but it won't work anymore.

When trying to load lumi I get the following error :

"Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'"

I removed the lumi package from my library and tried to reinstall it using

> source("http://bioconductor.org/biocLite.R")

> biocLite("lumi")

"Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'

According to some threads on different websites (http://seqanswers.com/forums/showthread.php?t=47785 particularly), RSQLite was updated to version 1.0.0 on October 25th, 2014 and this version of the package no longer contains the function "sqliteQuickSQL".

So I removed the current version of RSQLite that I must have updated since October 25th, and reinstalled the previous version (0.11.4), and then tried to reinstall lumi again.

After succesfully reinstalling lumi, under the 0.11.4 RSQLite version, I tried to load it

> library(lumi)

But I ended up with the error I had at the beginning :

"Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'"

I do not know what to do to make it work, and I would greatly appreciate any help that you could provide.

Lucas

lumi • 9.4k views
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Hi

I have the same problem, but I'm wanting to use 'CummeRbund', the main problem I have when trying to install the following packages Gviz, GenomicFeatures etc, is

Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'

based on the answers below the problem is the version of R, but I can't get the latest. I'm using Fedora 18, I have uninstalled, reinstalled, updated R (yum update R, etc) but I can only get verison  3.0.2-1.fc18. Does this mean I have to upgrade my operating system to get Bioconductor to work?

As described below I have updated, reinstalled Bioconductor

> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.

Is there a way to install the latest version or R without using Fedora repos??

thanks in advance and sorry if this is a stupid question but this is the third night I've been struggling with this

Steven

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You can always build the latest version of R yourself without waiting for it to propagate to the yum servers (note that there may be a way to get updated versions of R from yum, but not having used Fedora in about 10 years, I am not sure how one might go about doing such a thing).

Anyway, the way I usually install R (on Ubuntu, where I am not admin) is to download the sources from CRAN, untar in my home dir, and then build and make in place:

wget http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz
tar xvfz R-3.1.2.tar.gz
cd R-3.1.2
./configure
make

And if you have sudo privileges, you can also install to your system-wide directories using

sudo make install

Or you could just add the ~/R-3.2.1/bin directory to your PATH (at the beginning of the path), or you could do

sudo ln -s /usr/bin/R-3.1.2 /path/to/home/R-3.1.2/bin/R

which is nice if you want/need to keep different versions of R laying about.

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HI Dan

thanks for the advice. I downloaded the tar.gz, unpacked and hit make but I had a slight problem it wouldn't make and the source of the problem was

but this was fixed using

Then everything worked and I have now installed Biocondctor and CummeRbund and everything is working now (fingers crossed). I thought I'd mention the above incase anyone else reads this and has the same problem, with Fedora

Once again many thanks Steven

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Glad to hear it! Jim is the one you can thank. ;-)

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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 19 months ago
United States

You should update to Bioconductor 3.0 / R-3.1.2. Changes for compatibility with RSQLite_1.0.0 have only been made in Bioconductor 3.0 and the devel version (3.1).

So install R-3.1.2 and then do this:

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

If you see a message that says "Bioconductor version 2.14", do this:

biocLite("BiocUpgrade")

Then try installing lumi:

biocLite("lumi")

Dan

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lucashusquin ▴ 10
@lucashusquin-6959
Last seen 7.9 years ago
France

I followed your steps and updated to a newer R-version, but I still have the error while trying to install the lumi package.

"Error : l'objet ‘sqliteQuickSQL’ n'est pas exporté par 'namespace:RSQLite'"

> sessionInfo()

R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] Biobase_2.22.0       BiocGenerics_0.8.0   RSQLite_1.0.0
[4] DBI_0.3.1            BiocInstaller_1.16.0

loaded via a namespace (and not attached):
[1] affy_1.40.0           affyio_1.30.0         annotate_1.40.1
[4] AnnotationDbi_1.24.0  base64_1.1            beanplot_1.2
[7] Biostrings_2.30.1     bumphunter_1.2.0      codetools_0.2-8
[10] colorspace_1.2-4      digest_0.6.4          doRNG_1.6
[13] foreach_1.4.2         genefilter_1.44.0     GenomicRanges_1.14.4
[16] grid_3.1.1            illuminaio_0.4.0      IRanges_1.20.7
[19] iterators_1.0.7       itertools_0.1-3       KernSmooth_2.23-10
[22] lattice_0.20-24       limma_3.18.13         locfit_1.5-9.1
[25] MASS_7.3-29           Matrix_1.1-2          matrixStats_0.10.3
[28] mclust_4.4            methylumi_2.8.0       mgcv_1.7-28
[31] minfi_1.8.9           multtest_2.18.0       nleqslv_2.5
[34] nlme_3.1-113          nor1mix_1.2-0         pkgmaker_0.22
[37] plyr_1.8.1            preprocessCore_1.24.0 RColorBrewer_1.0-5
[40] Rcpp_0.11.3           registry_0.2          reshape_0.8.5
[43] R.methodsS3_1.6.1     rngtools_1.2.4        siggenes_1.36.0
[46] splines_3.1.1         stats4_3.1.1          stringr_0.6.2
[49] survival_2.37-7       tcltk_3.1.1           tools_3.1.1
[52] XML_3.98-1.1          xtable_1.7-4          XVector_0.2.0
[55] zlibbioc_1.8.0

Do you have any other suggestions ?

Lucas

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I believe you missed the

biocLite("BiocUpgrade")

step.

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Erreur : Bioconductor version 3.0 cannot be upgraded with R version 3.1.0

Lucas

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@james-w-macdonald-5106
Last seen 1 day ago
United States

It looks like you have a mix-n-match Bioconductor installation. You shouldn't have an RSQLite version anywhere near 1.0.0 with that old an R version. At this point I wouldn't even bother trying to fix your current R, but instead you should install R-3.1.1 and install Bioconductor from scratch using biocLite().

If you really want to use an old R-version, you can do

library(BiocInstaller)
biocValid()
biocLite()

Which will tell you which packages are off (biocValid()), and should install the correct ones (biocLite()). For those packages that are too new, biocValid() will tell you how to downgrade as well.

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Jim, RSQLite is a CRAN package, so all versions of BioC are equally hosed by 1.0.0 (except 3.0 and 3.1 which have been fixed to deal with it).

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Thanks for the pointer, Dan.

That's really unfortunate. I was under the mistaken impression that biocLite() did some version checking for CRAN packages as well. And note I am not saying anything, I'm just sayin'.

The reason this is unfortunate is because I (and possibly others) am often asked to do additional things for existing analyses. I try to follow the tenets of reproducible research by using Sweave files and dropping a sessionInfo() at the end so I can see what version I used. So when I need to add something to an analysis I did 2 years ago (yes, this happens, and yes, way more often than one would imagine...), I almost always add the extra bits to the Sweave document and re-run with whatever version of R/BioC I originally used. So I have lots of old R/BioC versions that I use semi-regularly.

And sometimes I have to install an additional package, which if it comes from BioC will be the correct package for that version of R/BioC, but if it comes from CRAN will most assuredly not be, particularly in the case of RSQLite.

So all future versions of me will have to remember to say 'n' when biocLite() helpfully asks if I want to update all these other packages when installing a package to an old install of R/BioC.

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Jim, we've discussed hosting a "frozen" CRAN repos that would be intended for use with a specific version of BioC.

I did make a snapshot of CRAN (pre-RSQLite_1.0.0) but haven't deployed it yet.

We did decide that we probably would not make these snapshots for no-longer-current versions of BioC, but that we'll do them going forward.

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Nice! I can see that making snapshots of long-since-gone versions of BioC isn't worth the trouble, but it will be nice to have the snapshots going forward.

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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 19 months ago
United States

biocLite()

And answer "a" when prompted to update all outdated packages. That should fix it.

Dan

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lucashusquin ▴ 10
@lucashusquin-6959
Last seen 7.9 years ago
France

Dan, using biocLite() returns an error :

> biocLite()

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1.
Message d'avis :
installed directory not writable, cannot update packages 'affy', 'affyio',
'annotate', 'AnnotationDbi', 'AnnotationForge', 'Biobase', 'BiocGenerics',
'BiocInstaller', 'bioDist', 'biomaRt', 'Biostrings', 'boot', 'BSgenome',
'BSgenome.Hsapiens.UCSC.hg19', 'bumphunter', 'class', 'cluster', 'codetools',
'FDb.InfiniumMethylation.hg19', 'foreign', 'genefilter', 'GenomicFeatures',
'GenomicRanges', 'illuminaio', 'IRanges', 'KernSmooth', 'lattice', 'limma',
'lumi', 'MASS', 'Matrix', 'methylumi', 'mgcv', 'minfi', 'minfiData',
'multtest', 'nlme', 'nnet', 'org.Hs.eg.db', 'preprocessCore', 'rpart',
'Rsamtools', 'RSQLite', 'rtracklayer', 'siggenes', 'spatial', 'sva',
'XVector', 'zlibbioc'

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Do you have root access on the machine? If so, run R as root:

sudo R

and try the same command.

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It worked and all the packages were updated, but I still couldn't load the lumi package afterwards (same error message).

Do you have any other ideas ? It's 7:30pm here though so I will look at your answers over the week end, thank you again for your help and your time.

Lucas

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Also, you seem to have a lot of packages loaded, try starting R as follows:

R --vanilla

and trying to install lumi as follows:

library(BiocInstaller)

biocLite("lumi")

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Hello Dan,

Thanks a lot it worked this time !

Lucas

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laseaman • 0
@laseaman-7727
Last seen 7.4 years ago
United States

I was having this same problem (the cummeRbund version) and because I was working on a server I did not have the permissions to update the packages. I found a workaround though. If you just run these two lines, before running the readCufflinks command after library(cummeRbund) it should work. I think it would likely help with the original lumi error but I wasn't having that problem so I don't know for sure.

sqliteQuickSQL<-dbGetQuery
dbBeginTransaction<-dbBegin