I got a parsing error when using pathview package to visualize pathways in my RNAseq data. This error still showed up even I tried to run the example (quick start with demo data) in the vignette. I found that XML was loaded successfully as shown in sessionInfo. Could someone help me to see what's wrong? Thank you very much!
> library(pathview)
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package
arallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'.
To cite Bioconductor, see 'citation("Biobase")', and for packages
'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
> data(gse16873.d)
> pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = "04110", species = "hsa", out.suffix = "gse16873")
Info: Downloading xml files for hsa04110, 1/1 pathways..
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Parsing ./hsa04110.xml file failed, please check the file!
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] pathview_1.16.1 org.Hs.eg.db_3.4.1 AnnotationDbi_1.38.1
[4] IRanges_2.10.2 S4Vectors_0.14.3 Biobase_2.36.2
[7] BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] graph_1.54.0 Rcpp_0.12.12 KEGGgraph_1.38.0 XVector_0.16.0
[5] zlibbioc_1.22.0 bit_1.1-12 R6_2.2.2 rlang_0.1.1
[9] blob_1.1.0 httr_1.2.1 tools_3.4.1 grid_3.4.1
[13] png_0.1-7 DBI_0.7 bit64_0.9-7 digest_0.6.12
[17] tibble_1.3.3 Rgraphviz_2.20.0 KEGGREST_1.16.0 memoise_1.1.0
[21] RSQLite_2.0 compiler_3.4.1 Biostrings_2.44.1 XML_3.98-1.9
[25] pkgconfig_2.0.1
> library(pathview)
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package
![Stick Out Tongue](https://www.seqanswers.com/core/images/smilies/tongue.png)
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'.
To cite Bioconductor, see 'citation("Biobase")', and for packages
'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
> data(gse16873.d)
> pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = "04110", species = "hsa", out.suffix = "gse16873")
Info: Downloading xml files for hsa04110, 1/1 pathways..
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Parsing ./hsa04110.xml file failed, please check the file!
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] pathview_1.16.1 org.Hs.eg.db_3.4.1 AnnotationDbi_1.38.1
[4] IRanges_2.10.2 S4Vectors_0.14.3 Biobase_2.36.2
[7] BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] graph_1.54.0 Rcpp_0.12.12 KEGGgraph_1.38.0 XVector_0.16.0
[5] zlibbioc_1.22.0 bit_1.1-12 R6_2.2.2 rlang_0.1.1
[9] blob_1.1.0 httr_1.2.1 tools_3.4.1 grid_3.4.1
[13] png_0.1-7 DBI_0.7 bit64_0.9-7 digest_0.6.12
[17] tibble_1.3.3 Rgraphviz_2.20.0 KEGGREST_1.16.0 memoise_1.1.0
[21] RSQLite_2.0 compiler_3.4.1 Biostrings_2.44.1 XML_3.98-1.9
[25] pkgconfig_2.0.1
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