Last updated on 2019-04-28 11:50:30 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-fedora-clang | 0.5.5 | 68.28 | ERROR | |||
| r-patched-solaris-x86 | 0.5.5 | 76.60 | ERROR |
Version: 0.5.5
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘purrr’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86
Version: 0.5.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [24s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(NACHO)
>
> test_check("NACHO")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/matrix/GSE74821_series_matrix.txt.gz'
Content type 'application/x-gzip' length 488690 bytes (477 KB)
==================================================
downloaded 477 KB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/suppl//GSE74821_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 2713600 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/suppl//GSE74821_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 2713600 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/suppl//GSE74821_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 2713600 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/suppl//GSE74821_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 2713600 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/suppl//GSE74821_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 2713600 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/suppl//GSE74821_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 2713600 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
── 1. Error: using GEO GSE74821 with prediction (@test-summarise.R#144) ───────
HTTP error 403.
1: GEOquery::getGEO(GEO = "GSE74821") at testthat/test-summarise.R:144
2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics)
3: getDirListing(sprintf(gdsurl, stub, GEO))
4: xml2::read_html(url)
5: read_html.default(url)
6: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
10: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x,
options = options)
11: open(x, "rb")
12: open.connection(x, "rb")
── 2. Error: using GEO GSE70970 (@test-summarise.R#168) ───────────────────────
HTTP error 403.
1: GEOquery::getGEO(GEO = "GSE70970") at testthat/test-summarise.R:168
2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics)
3: getDirListing(sprintf(gdsurl, stub, GEO))
4: xml2::read_html(url)
5: read_html.default(url)
6: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
10: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x,
options = options)
11: open(x, "rb")
12: open.connection(x, "rb")
── 3. Error: using GEO GSE70970 with prediction (@test-summarise.R#191) ───────
HTTP error 403.
1: GEOquery::getGEO(GEO = "GSE70970") at testthat/test-summarise.R:191
2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics)
3: getDirListing(sprintf(gdsurl, stub, GEO))
4: xml2::read_html(url)
5: read_html.default(url)
6: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
10: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x,
options = options)
11: open(x, "rb")
12: open.connection(x, "rb")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 36 SKIPPED: 0 WARNINGS: 0 FAILED: 3
1. Error: using GEO GSE74821 with prediction (@test-summarise.R#144)
2. Error: using GEO GSE70970 (@test-summarise.R#168)
3. Error: using GEO GSE70970 with prediction (@test-summarise.R#191)
Error: testthat unit tests failed
In addition: Warning messages:
1: In is.function(FUN) :
closing unused connection 6 (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/matrix/)
2: In is.function(FUN) :
closing unused connection 5 (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/matrix/)
3: In is.function(FUN) :
closing unused connection 4 (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/matrix/)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.5.5
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘NACHO.Rmd’ using rmarkdown
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
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':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect,
is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Warning in 10L %in% opts :
closing unused connection 5 (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/matrix/)
No supplemental files found.
Check URL manually if in doubt
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/suppl/
/usr/bin/gtar: /tmp/Rtmp9zSRRc/GSE70970/GSE70970_RAW.tar: Cannot open: No such file or directory
/usr/bin/gtar: Error is not recoverable: exiting now
Warning in untar(tarfile = paste0(tempdir(), "/GSE70970/GSE70970_RAW.tar"), :
'/usr/bin/gtar -xf '/tmp/Rtmp9zSRRc/GSE70970/GSE70970_RAW.tar' -C '/tmp/Rtmp9zSRRc/GSE70970/Data'' returned error code 2
Quitting from lines 170-171 (NACHO.Rmd)
Error: processing vignette 'NACHO.Rmd' failed with diagnostics:
object 'GSE70970_sum' not found
--- failed re-building ‘NACHO.Rmd’
SUMMARY: processing the following file failed:
‘NACHO.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.5.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/118s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(NACHO)
>
> test_check("NACHO")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/matrix/GSE74821_series_matrix.txt.gz'
Content type 'application/x-gzip' length 488690 bytes (477 KB)
==================================================
downloaded 477 KB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/suppl//GSE74821_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 2713600 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74821/suppl//GSE74821_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 2713600 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
── 1. Error: no housekeeping norm (@test-summarise.R#73) ──────────────────────
HTTP error 403.
1: GEOquery::getGEO(GEO = "GSE74821") at testthat/test-summarise.R:73
2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics)
3: getDirListing(sprintf(gdsurl, stub, GEO))
4: xml2::read_html(url)
5: read_html.default(url)
6: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
10: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x,
options = options)
11: open(x, "rb")
12: open.connection(x, "rb")
── 2. Error: no housekeeping norm and prediction (@test-summarise.R#96) ───────
HTTP error 403.
1: GEOquery::getGEO(GEO = "GSE74821") at testthat/test-summarise.R:96
2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics)
3: getDirListing(sprintf(gdsurl, stub, GEO))
4: xml2::read_html(url)
5: read_html.default(url)
6: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
10: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x,
options = options)
11: open(x, "rb")
12: open.connection(x, "rb")
── 3. Error: using GEO GSE74821 (@test-summarise.R#121) ───────────────────────
HTTP error 403.
1: GEOquery::getGEO(GEO = "GSE74821") at testthat/test-summarise.R:121
2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics)
3: getDirListing(sprintf(gdsurl, stub, GEO))
4: xml2::read_html(url)
5: read_html.default(url)
6: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
10: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x,
options = options)
11: open(x, "rb")
12: open.connection(x, "rb")
── 4. Error: using GEO GSE74821 with prediction (@test-summarise.R#144) ───────
HTTP error 403.
1: GEOquery::getGEO(GEO = "GSE74821") at testthat/test-summarise.R:144
2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics)
3: getDirListing(sprintf(gdsurl, stub, GEO))
4: xml2::read_html(url)
5: read_html.default(url)
6: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
10: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x,
options = options)
11: open(x, "rb")
12: open.connection(x, "rb")
── 5. Error: using GEO GSE70970 (@test-summarise.R#168) ───────────────────────
HTTP error 403.
1: GEOquery::getGEO(GEO = "GSE70970") at testthat/test-summarise.R:168
2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics)
3: getDirListing(sprintf(gdsurl, stub, GEO))
4: xml2::read_html(url)
5: read_html.default(url)
6: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
10: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x,
options = options)
11: open(x, "rb")
12: open.connection(x, "rb")
── 6. Error: using GEO GSE70970 with prediction (@test-summarise.R#191) ───────
HTTP error 403.
1: GEOquery::getGEO(GEO = "GSE70970") at testthat/test-summarise.R:191
2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics)
3: getDirListing(sprintf(gdsurl, stub, GEO))
4: xml2::read_html(url)
5: read_html.default(url)
6: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
8: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
10: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x,
options = options)
11: open(x, "rb")
12: open.connection(x, "rb")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 33 SKIPPED: 0 WARNINGS: 0 FAILED: 6
1. Error: no housekeeping norm (@test-summarise.R#73)
2. Error: no housekeeping norm and prediction (@test-summarise.R#96)
3. Error: using GEO GSE74821 (@test-summarise.R#121)
4. Error: using GEO GSE74821 with prediction (@test-summarise.R#144)
5. Error: using GEO GSE70970 (@test-summarise.R#168)
6. Error: using GEO GSE70970 with prediction (@test-summarise.R#191)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.5.5
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘NACHO.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
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':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect,
is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No supplemental files found.
Check URL manually if in doubt
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/suppl/
/opt/csw/bin/gtar: /tmp/Rtmp.qa4lc/GSE70970/GSE70970_RAW.tar: Cannot open: No such file or directory
/opt/csw/bin/gtar: Error is not recoverable: exiting now
Warning in untar(tarfile = paste0(tempdir(), "/GSE70970/GSE70970_RAW.tar"), :
'/opt/csw/bin/gtar -xf '/tmp/Rtmp.qa4lc/GSE70970/GSE70970_RAW.tar' -C '/tmp/Rtmp.qa4lc/GSE70970/Data'' returned error code 2
Warning in name :
closing unused connection 6 (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/suppl/)
Warning in name :
closing unused connection 5 (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/matrix/)
Quitting from lines 170-171 (NACHO.Rmd)
Error: processing vignette 'NACHO.Rmd' failed with diagnostics:
object 'GSE70970_sum' not found
--- failed re-building ‘NACHO.Rmd’
SUMMARY: processing the following file failed:
‘NACHO.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86