Also note that, according to the sessionInfo() you sent, it seems you
were using the release. I've no idea how you could get these warnings
with the release since the changes I made recently to AnnotationDbi,
Category, and GOstats are in devel only...
H.
On 09/23/2014 11:05 AM, James W. MacDonald wrote:
Never mind. Installing all of GOstats, Category, AnnotationDbi and
ReportingTools fixed the issue.
Thanks,
Jim
On Tue, Sep 23, 2014 at 1:55 PM, James W. MacDonald <jmacdon at uw.edu
<mailto:jmacdon at uw.edu>> wrote:
Hi Herve,
No joy:
> biocLite("ReportingTools")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
3.1.0.
Installing package(s) 'ReportingTools'
trying URL
'http://bioconductor.org/packages/2.14/bioc/src/
contrib/ReportingTools_2.4.0.tar.gz'
Content type 'application/x-gzip' length 2570348 bytes (2.5 Mb)
opened URL
==================================================
downloaded 2.5 Mb
* installing *source* package ?ReportingTools? ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, :
No generic function found corresponding to requested imported
methods for "summary" from package "AnnotationDbi" (malformed
exports?)
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, :
No generic function found corresponding to requested imported
methods for "summary" from package "Category" (malformed exports?)
Warning: found methods to import for function ?summary? but not the
generic itself
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, :
No generic function found corresponding to requested imported
methods for "summary" from package "GOstats" (malformed exports?)
Warning: found methods to import for function ?summary? but not the
generic itself
in method for ?objectToHTML? with signature ?object="ggbio"?: no
definition for class ?ggbio?
Note: no visible binding for '<<-' assignment to '.reportDirectory'
Note: no visible binding for '<<-' assignment to '.reportDirectory'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, :
No generic function found corresponding to requested imported
methods for "summary" from package "AnnotationDbi" (malformed
exports?)
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, :
No generic function found corresponding to requested imported
methods for "summary" from package "Category" (malformed exports?)
Warning: found methods to import for function ?summary? but not the
generic itself
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, :
No generic function found corresponding to requested imported
methods for "summary" from package "GOstats" (malformed exports?)
Warning: found methods to import for function ?summary? but not the
generic itself
* DONE (ReportingTools)
And when I load ReportingTools I still get the warnings:
Warning messages:
1: In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, :
No generic function found corresponding to requested imported
methods for "summary" from package "AnnotationDbi" (malformed
exports?)
2: In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, :
No generic function found corresponding to requested imported
methods for "summary" from package "Category" (malformed exports?)
3: found methods to import for function ?summary? but not the
generic itself
4: In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, :
No generic function found corresponding to requested imported
methods for "summary" from package "GOstats" (malformed exports?)
5: found methods to import for function ?summary? but not the
generic itself
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] ReportingTools_2.4.0 AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2
[4] Biobase_2.24.0 BiocGenerics_0.10.0 RSQLite_0.11.4
[7] DBI_0.3.0 knitr_1.6 BiocInstaller_1.14.2
loaded via a namespace (and not attached):
[1] annotate_1.42.1 AnnotationForge_1.6.1 BatchJobs_1.3
[4] BBmisc_1.7 BiocParallel_0.6.1 biomaRt_2.20.0
[7] Biostrings_2.32.1 biovizBase_1.12.3 bitops_1.0-6
[10] brew_1.0-6 BSgenome_1.32.0 Category_2.30.0
[13] checkmate_1.4 cluster_1.15.2 codetools_0.2-9
[16] colorspace_1.2-4 DESeq2_1.4.5 dichromat_2.0-0
[19] digest_0.6.4 edgeR_3.6.8 evaluate_0.5.5
[22] fail_1.2 foreach_1.4.2 formatR_1.0
[25] Formula_1.1-2 genefilter_1.46.1
geneplotter_1.42.0
[28] GenomicAlignments_1.0.6 GenomicFeatures_1.16.2
GenomicRanges_1.16.4
[31] ggbio_1.12.10 ggplot2_1.0.0 GO.db_2.14.0
[34] GOstats_2.30.0 graph_1.42.0 grid_3.1.0
[37] gridExtra_0.9.1 GSEABase_1.26.0 gtable_0.1.2
[40] Hmisc_3.14-4 hwriter_1.3.1 IRanges_1.22.10
[43] iterators_1.0.7 lattice_0.20-29
latticeExtra_0.6-26
[46] limma_3.20.9 locfit_1.5-9.1 MASS_7.3-34
[49] Matrix_1.1-4 munsell_0.4.2 PFAM.db_2.14.0
[52] plyr_1.8.1 proto_0.3-10 RBGL_1.40.1
[55] RColorBrewer_1.0-5 Rcpp_0.11.2
RcppArmadillo_0.4.400.0
[58] RCurl_1.95-4.3 reshape2_1.4
R.methodsS3_1.6.1
[61] R.oo_1.18.0 Rsamtools_1.16.1
rtracklayer_1.24.2
[64] R.utils_1.33.0 scales_0.2.4 sendmailR_1.1-2
[67] splines_3.1.0 stats4_3.1.0 stringr_0.6.2
[70] survival_2.37-7 tools_3.1.0
VariantAnnotation_1.10.5
[73] XML_3.98-1.1 xtable_1.7-3 XVector_0.4.0
[76] zlibbioc_1.10.0
Jim
On Tue, Sep 23, 2014 at 1:43 PM, Herv? Pag?s <hpages at fhcrc.org
<mailto:hpages at fhcrc.org>> wrote:
Hi Jim,
On 09/23/2014 09:42 AM, James W. MacDonald wrote:
There is an issue on the support site having to do with the
inability to
import the summary function from the namespaces from the
packages listed in
the subject line. I see the same problem/errors with my
affycoretools
package.
When you load ReportingTools, you get the following warnings:
Warning messages:
1: In namespaceImportMethods(ns, loadNamespace(j <-
imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested
imported methods for
"summary" from package "AnnotationDbi" (malformed exports?)
2: In namespaceImportMethods(ns, loadNamespace(j <-
imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested
imported methods for
"summary" from package "Category" (malformed exports?)
3: In namespaceImportMethods(ns, loadNamespace(j <-
imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested
imported methods for
"summary" from package "GOstats" (malformed exports?)
Is this because of the following changes?
------------------------------__----------------------------
--__------------
r94092 | hpages at fhcrc.org <mailto:hpages at fhcrc.org> |
2014-09-12 18:02:34 -0700 (Fri, 12 Sep 2014) |
7 lines
Changed paths:
M /trunk/madman/Rpacks/__AnnotationDbi/DESCRIPTION
M /trunk/madman/Rpacks/__AnnotationDbi/NAMESPACE
M
/trunk/madman/Rpacks/__AnnotationDbi/R/createAnnObjs-
__utils.R
M
/trunk/madman/Rpacks/__AnnotationDbi/R/createAnnObjs.
__NCBIORG_DBs.R
M
/trunk/madman/Rpacks/__AnnotationDbi/R/methods-__Inparanoid.R
M
/trunk/madman/Rpacks/__AnnotationDbi/R/methods-__
Inparanoid8.R
M
/trunk/madman/Rpacks/__AnnotationDbi/R/methods-__
geneCentricDbs.R
- Drop dependency on IRanges (stuff from IRanges needed by
AnnotationDbi is
now in S4Vectors).
- Add dependency on stats4 and import summary() from it.
This is an S4
generic and AnnotationDbi defines and exports S4 methods
for it.
- Address the "A package almost never needs to use ::: for
its own objects"
NOTE from 'R CMD check'.
which included
Index: NAMESPACE
==============================__============================
==__=======
--- NAMESPACE (revision 94000)
+++ NAMESPACE (working copy)
@@ -1,11 +1,11 @@
import(methods)
import(utils)
+importFrom(stats4, summary)
import(Biobase)
import(DBI)
import(RSQLite)
import(BiocGenerics)
-importFrom(S4Vectors, isTRUEorFALSE, isSingleString,
metadata)
-importFrom(IRanges, elementLengths)
+importFrom(S4Vectors, isTRUEorFALSE, isSingleString,
metadata,
elementLengths)
importFrom(GenomeInfoDb, genomeStyles, extractSeqlevels,
mapSeqlevels)
exportClasses(
@@ -169,9 +169,6 @@
intraIDMapper,
idConverter,
- #Needs to be exported from RSQLite
- summary,
-
## AnnotationDb
metadata,
so it appears summary is no longer exported?
Yes, no need to export summary from AnnotationDbi because
summary() is a
generic defined in the stats4 package. Before I made that change,
AnnotationDbi was implicitly promoting base::summary() to an S4
generic
which was then a different generic from stats4::summary().
Having these
2 distinct summary() generics was causing the usual troubles
when a
user had AnnotationDbi and stats4 in their search path. Also it
was
breaking the attract package in some obscure way.
The warnings you get when you load ReportingTools will hopefully
go away if you reinstall the package. Let me know if it doesn't.
Hope this helps,
H.
Best,
Jim
--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org <mailto:hpages at fhcrc.org>
Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319