Thomas Girke
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/eiR |
| Branch: RELEASE_3_8 |
| Last Commit: f11bf8f |
| Last Changed Date: 2018-10-30 11:41:51 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:46 -0400 (Sat, 13 Apr 2019).
| Package 462/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| eiR 1.22.0 Thomas Girke
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: eiR |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:eiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings eiR_1.22.0.tar.gz |
| StartedAt: 2019-04-13 02:01:13 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:06:21 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 307.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: eiR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:eiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings eiR_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/eiR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'eiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eiR' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'eiR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'methods' 'ChemmineR'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'BiocGenerics' 'RCurl' 'RUnit'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
insertEmbeddedDescriptors: no visible global function definition for
'postgresqlWriteTable'
insertEmbeddedDescriptorsByCompoundId: no visible global function
definition for 'postgresqlWriteTable'
insertGroupMembers: no visible global function definition for
'postgresqlWriteTable'
Undefined global functions or variables:
postgresqlWriteTable
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
FAILURE in test_ea.eiAdd: Error in checkEquals(results$distance[1], 0) :
Mean relative difference: 1
ERROR in test_fa.eiCluster: Error in neighbors[i, , 1] : subscript out of bounds
Test files with failing tests
test_main.R
test_ea.eiAdd
test_fa.eiCluster
Error in BiocGenerics:::testPackage("eiR") :
unit tests failed for package eiR
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/eiR.Rcheck/00check.log'
for details.
eiR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch eiR
###
##############################################################################
##############################################################################
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
* installing *source* package 'eiR' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c optimFunctions.cc -o optimFunctions.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o eiR.dll tmp.def optimFunctions.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.8-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/R/library/eiR/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'eiR'
finding HTML links ... done
addTransform html
eiAdd html
eiCluster html
eiInit html
finding level-2 HTML links ... done
eiMakeDb html
eiPerformanceTest html
eiQuery html
example_compounds html
freeLSHData html
loadLSHData html
setDefaultDistance html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (eiR)
Making 'packages.html' ... done
In R CMD INSTALL
eiR.Rcheck/tests/runTests.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("eiR")
test_main start
Loading required package: RSQLite
[1] "createing db"
/cygdrive/c/Rtools/bin/rm: cannot remove 'test_workspace/data/chem.db': Device or resource busy
eiInit tests
default descriptor
loaded 100 compounds
[1] "100 loaded by eiInit"
setting priorities for 4 groups.
fp descriptor
[1] "createing db"
using cluster
[1] 0
[1] "0 loaded by eiInit"
starting worker for localhost:11436
starting worker for localhost:11436
starting worker for localhost:11436
[1] "set1"
[1] 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218
[19] 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236
[37] 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254
[55] 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272
[73] 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290
[91] 291 292 293 294 295 296 297 298 299 300
[1] "set2"
[1] 201 202 205 208 209 210 211 217 218 219 220 223 224 225 226 229 231 233 234
[20] 236 238 243 245 246 247 248 249 251 253 266 267 270 271 272 273 274 275 277
[39] 278 279 280 281 282 283 287 288 289 291 299 300
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
evaluationg results
Type: EXEC
in indexProcessor: 1
[1] "partFilename: test_workspace/parDist.final.part-1"
starting
Loading required package: eiR
Loading required package: ChemmineR
Loading required package: DBI
Loading required package: RSQLite
in reduce
Type: DONE
Type: DONE
Type: DONE
eiMakeDb
starting worker for localhost:11436
[1] "by file name"
found 96 un-embedded descriptors for runId 1
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Loading required package: eiR
Loading required package: ChemmineR
Loading required package: DBI
Loading required package: RSQLite
Regenerating matrix file...
Regenerating matrix file...
found 50 refs
found 10 samples
checking descriptors
[1] "by number"
found 96 un-embedded descriptors for runId 2
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Regenerating matrix file...
Regenerating matrix file...
found 50 refs
found 20 samples
checking descriptors
[1] "by vector"
found 96 un-embedded descriptors for runId 3
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Regenerating matrix file...
Regenerating matrix file...
Type: DONE
found 50 refs
found 20 samples
checking descriptors
eiQuery
using runId 3
eiQuery test 1
creating annoy index
loading matrix file
done. num items in index: 96
found 2 queries
eiQuery test 2
creating annoy index
loading matrix file
done. num items in index: 96
found 2 queries
eiQuery test 3
creating annoy index
loading matrix file
done. num items in index: 96
found 2 queries
computing embedded distances on test quries
writing top 50000 to file test_workspace/run-50-40/eucsearch.50-40
A connection with
description "test_workspace/run-50-40/eucsearch.50-40"
class "file"
mode "w"
text "text"
opened "opened"
can read "no"
can write "yes"
[1] "getting test query ids"
writing top 50000 to file test_workspace/data/chemical-search.results
A connection with
description "test_workspace/data/chemical-search.results"
class "file"
mode "w"
text "text"
opened "opened"
can read "no"
can write "yes"
average embedding performance: 0.532485309920425
creating annoy index
loading matrix file
done. num items in index: 96
found 20 queries
average indexing performance: 0.79434327208131
checking chemical-search.results
[1] "searching for chemical-search.results$ expected dims: 20 96"
[1] "test_workspace/data/chemical-search.results"
[1] "found dims: 20" "found dims: 96"
checking eucsearch
[1] "searching for eucsearch.50-40 expected dims: 15 96"
[2] "searching for eucsearch.50-40 expected dims: 16 96"
[3] "searching for eucsearch.50-40 expected dims: 17 96"
[4] "searching for eucsearch.50-40 expected dims: 18 96"
[5] "searching for eucsearch.50-40 expected dims: 19 96"
[6] "searching for eucsearch.50-40 expected dims: 20 96"
[1] "test_workspace/run-50-40/eucsearch.50-40"
[1] "found dims: 20" "found dims: 96"
checking indexed.performance
[1] "searching for indexed.performance expected dims: 20 1"
[1] "test_workspace/run-50-40/indexed.performance"
[1] "found dims: 20" "found dims: 1"
using runId 3
eiAdd test1
loaded 2 compounds
[1] "2 loaded by eiInit"
setting priorities for 0 groups.
found 2 un-embedded descriptors for runId 3
Regenerating matrix file...
creating annoy index
loading matrix file
done. num items in index: 98
found 2 queries
query target distance target_ids
1 3540 3540 0.0000000 301
2 3540 650073 0.7848101 268
3 3540 650007 0.7940199 207
4 3540 650028 0.7989950 227
5 3540 650029 0.8048780 228
6 3540 650037 0.8093385 236
7 3540 650040 0.8093842 239
8 3540 650010 0.8098361 210
9 3540 650019 0.8116343 218
10 3540 650026 0.8141176 225
11 3540 650076 0.8169014 271
12 3540 650041 0.8175896 240
13 3540 650023 0.8252427 222
14 3540 650102 0.8280922 296
15 3540 650030 0.8293515 229
16 3540 650103 0.8312958 297
17 3540 650066 0.8312958 261
18 3540 650106 0.8328267 300
19 3540 650012 0.8341463 212
20 3540 650039 0.8356436 238
21 3540 650083 0.8360277 278
22 3540 650044 0.8410714 243
23 3540 650035 0.8412162 234
24 3540 650072 0.8426966 267
25 3540 650006 0.8428571 206
26 3540 650079 0.8440367 274
27 3540 650104 0.8443878 298
28 3540 650071 0.8468468 266
29 3540 650025 0.8486056 224
30 3540 650100 0.8493151 294
31 3540 650015 0.8502415 215
32 3540 650089 0.8502538 283
33 3540 650101 0.8512658 295
34 3540 650008 0.8513011 208
35 3540 650105 0.8515625 299
36 3540 650060 0.8528428 255
37 3540 650069 0.8539326 264
38 3540 650045 0.8548896 244
39 3540 650027 0.8560000 226
40 3540 650068 0.8568507 263
41 3540 650099 0.8573826 293
42 3540 650080 0.8580645 275
43 3540 650021 0.8591885 220
44 3540 5329468 0.8605341 302
45 3540 650095 0.8642384 289
46 3540 650047 0.8666667 246
47 3540 650062 0.8671329 257
48 3540 650078 0.8671329 273
49 3540 650003 0.8672986 203
50 3540 650024 0.8672986 223
51 3540 650098 0.8690808 292
52 3540 650009 0.8691589 209
53 3540 650002 0.8699764 202
54 3540 650042 0.8752941 241
55 3540 650048 0.8763636 247
56 3540 650034 0.8765432 233
57 3540 650082 0.8778626 277
58 3540 650016 0.8787129 216
59 3540 650058 0.8814815 253
60 3540 650091 0.8820000 285
61 3540 650011 0.8862020 211
62 3540 650017 0.8865979 217
63 3540 650001 0.8872549 201
64 3540 650093 0.8876712 287
65 3540 650013 0.8883721 213
66 3540 650067 0.8885587 262
67 3540 650014 0.8902439 214
68 3540 650092 0.8909348 286
69 3540 650085 0.8924915 279
70 3540 650090 0.8926554 284
71 3540 650038 0.8932927 237
72 3540 650074 0.8951256 269
73 3540 650096 0.8967391 290
74 3540 650032 0.8981324 231
75 3540 650031 0.8992806 230
76 3540 650005 0.8997290 205
77 3540 650081 0.9028571 276
78 3540 650022 0.9031477 221
79 3540 650094 0.9037162 288
80 3540 650020 0.9057971 219
81 3540 650033 0.9074074 232
82 3540 650064 0.9084337 259
83 3540 650077 0.9086758 272
84 3540 650097 0.9090909 291
85 3540 650075 0.9100529 270
86 3540 650004 0.9110738 204
87 3540 650070 0.9118852 265
88 3540 650086 0.9139241 280
89 3540 650049 0.9191686 248
90 3540 650054 0.9214502 251
91 3540 650046 0.9229711 245
92 3540 650050 0.9239905 249
93 3540 650036 0.9292035 235
94 3540 650056 0.9386282 252
95 3540 650087 0.9391101 281
96 3540 650088 0.9411765 282
97 3540 650052 0.9681529 250
98 3540 650043 0.9851301 242
99 5329468 5329468 0.0000000 302
100 5329468 650045 0.5728155 244
101 5329468 650101 0.6554878 295
102 5329468 650100 0.6772727 294
103 5329468 650030 0.7006173 229
104 5329468 650012 0.7449210 212
105 5329468 650104 0.7505882 298
106 5329468 650076 0.7510730 271
107 5329468 650040 0.7525773 239
108 5329468 650066 0.7561521 261
109 5329468 650019 0.7634146 218
110 5329468 650010 0.7681564 210
111 5329468 650025 0.7684564 224
112 5329468 650037 0.7692308 236
113 5329468 650099 0.7698541 293
114 5329468 650105 0.7779817 299
115 5329468 650007 0.7783934 207
116 5329468 650047 0.7807309 246
117 5329468 650096 0.7808564 290
118 5329468 650073 0.7810026 268
119 5329468 650008 0.7895652 208
120 5329468 650069 0.7963526 264
121 5329468 650090 0.7978339 284
122 5329468 650026 0.8000000 225
123 5329468 650011 0.8025035 211
124 5329468 650041 0.8113208 240
125 5329468 650015 0.8125937 215
126 5329468 650028 0.8144989 227
127 5329468 650046 0.8156809 245
128 5329468 650038 0.8208556 237
129 5329468 650072 0.8263069 267
130 5329468 650054 0.8284024 251
131 5329468 650039 0.8295255 238
132 5329468 650092 0.8333333 286
133 5329468 650068 0.8375912 263
134 5329468 650082 0.8376963 277
135 5329468 650048 0.8438538 247
136 5329468 650032 0.8460317 231
137 5329468 650009 0.8485640 209
138 5329468 650016 0.8506494 216
139 5329468 650106 0.8535980 300
140 5329468 650003 0.8559671 203
141 5329468 650036 0.8575130 235
142 5329468 650075 0.8590164 270
143 5329468 650081 0.8592593 276
144 5329468 650080 0.8595506 275
145 5329468 650102 0.8604651 296
146 5329468 650085 0.8605016 279
147 5329468 3540 0.8605341 301
148 5329468 650013 0.8653061 213
149 5329468 650033 0.8701299 232
150 5329468 650050 0.8702128 249
151 5329468 650035 0.8713137 234
152 5329468 650049 0.8719008 248
153 5329468 650044 0.8728682 243
154 5329468 650074 0.8731241 269
155 5329468 650014 0.8785942 214
156 5329468 650079 0.8786127 274
157 5329468 650077 0.8790323 272
158 5329468 650027 0.8807947 226
159 5329468 650097 0.8825503 291
160 5329468 650029 0.8832891 228
161 5329468 650071 0.8840580 266
162 5329468 650098 0.8847926 292
163 5329468 650002 0.8857715 202
164 5329468 650006 0.8864266 206
165 5329468 650058 0.8867925 253
166 5329468 650070 0.8886861 265
167 5329468 650004 0.8900763 204
168 5329468 650103 0.8902196 297
169 5329468 650001 0.8919708 201
170 5329468 650067 0.8927614 262
171 5329468 650095 0.8950131 289
172 5329468 650078 0.8956044 273
173 5329468 650022 0.8960499 221
174 5329468 650094 0.8968134 288
175 5329468 650086 0.8978261 280
176 5329468 650060 0.8979058 255
177 5329468 650093 0.9000000 287
178 5329468 650021 0.9011858 220
179 5329468 650089 0.9028926 283
180 5329468 650034 0.9133127 233
181 5329468 650042 0.9140625 241
182 5329468 650056 0.9153094 252
183 5329468 650083 0.9182156 278
184 5329468 650024 0.9182879 223
185 5329468 650062 0.9222520 257
186 5329468 650087 0.9229209 281
187 5329468 650064 0.9272727 259
188 5329468 650091 0.9294118 285
189 5329468 650088 0.9343629 282
190 5329468 650023 0.9347826 222
191 5329468 650017 0.9448819 217
192 5329468 650020 0.9464286 219
193 5329468 650031 0.9508197 230
194 5329468 650052 0.9744898 250
195 5329468 650005 0.9789030 205
196 5329468 650043 1.0000000 242
checking descriptors
eiAdd test2
loaded 5 compounds
[1] "5 loaded by eiInit"
setting priorities for 0 groups.
found 5 un-embedded descriptors for runId 3
Regenerating matrix file...
creating annoy index
loading matrix file
done. num items in index: 98
found 1 queries
Timing stopped at: 0.81 0.13 6.39
Error in checkEquals(results$distance[1], 0) :
Mean relative difference: 1
In addition: Warning messages:
1: In dir.create(test_dir) : 'test_workspace' already exists
2: call dbDisconnect() when finished working with a connection
creating annoy index
test_workspace/run-50-40/matrix.50-404010-1
loading matrix file
done. num items in index: 98
Timing stopped at: 0.47 0 0.47
Error in neighbors[i, , 1] : subscript out of bounds
RUNIT TEST PROTOCOL -- Sat Apr 13 02:06:16 2019
***********************************************
Number of test functions: 8
Number of errors: 1
Number of failures: 1
1 Test Suite :
eiR RUnit Tests - 8 test functions, 1 error, 1 failure
FAILURE in test_ea.eiAdd: Error in checkEquals(results$distance[1], 0) :
Mean relative difference: 1
ERROR in test_fa.eiCluster: Error in neighbors[i, , 1] : subscript out of bounds
Test files with failing tests
test_main.R
test_ea.eiAdd
test_fa.eiCluster
Error in BiocGenerics:::testPackage("eiR") :
unit tests failed for package eiR
Execution halted
eiR.Rcheck/eiR-Ex.timings
| name | user | system | elapsed | |
| addTransform | 0 | 0 | 0 | |
| eiAdd | 3.27 | 1.32 | 4.67 | |
| eiCluster | 2.72 | 1.55 | 4.41 | |
| eiInit | 1.05 | 0.08 | 1.12 | |
| eiMakeDb | 2.32 | 1.73 | 4.15 | |
| eiPerformanceTest | 3.17 | 1.53 | 4.83 | |
| eiQuery | 2.95 | 1.72 | 4.78 | |
| freeLSHData | 0 | 0 | 0 | |
| loadLSHData | 0 | 0 | 0 | |
| setDefaultDistance | 0 | 0 | 0 | |