| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:09 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE Mirsynergy PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1100/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Mirsynergy 1.24.0 Yue Li
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK |
| Package: Mirsynergy |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mirsynergy.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Mirsynergy_1.24.0.tar.gz |
| StartedAt: 2020-10-17 06:08:23 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:10:05 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 101.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Mirsynergy.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mirsynergy.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Mirsynergy_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Mirsynergy.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Mirsynergy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Mirsynergy' version '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Mirsynergy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'Mirsynergy-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mirsynergy
> ### Title: Detect synergistic miRNA regulatory modules by overlapping
> ### neighbourhood expansion
> ### Aliases: mirsynergy
> ### Keywords: clustering microRNA
>
> ### ** Examples
>
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==> Define data, use random,
> ##-- or do help(data=index) for the standard data sets.
> ##
> # simulate N mRNA and M miRNA and their interaction matrices
> load(system.file("extdata/toy_modules.RData", package="Mirsynergy"))
>
> # run mirsynergy clustering
> V <- mirsynergy(W, H, verbose=TRUE)
Discard row/column of all zeros in W
*Stage I. Cluster 18 miRNA:
Forming new module with seed: miRNA6
add: miRNA18; w.in: 0.655; w.bound: 1.535; new synergy: 0.106
add: miRNA8; w.in: 1.152; w.bound: 1.460; new synergy: 0.134
add: miRNA12; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA3
add: miRNA9; w.in: 0.735; w.bound: 0.484; new synergy: 0.141
Forming new module with seed: miRNA17
add: miRNA2; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA2
add: miRNA17; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA10
add: miRNA15; w.in: 0.304; w.bound: 0.532; new synergy: 0.063
add: miRNA14; w.in: 0.573; w.bound: 0.649; new synergy: 0.079
add: miRNA17; w.in: 0.796; w.bound: 1.120; new synergy: 0.080
add: miRNA2; w.in: 1.233; w.bound: 1.149; new synergy: 0.100
Forming new module with seed: miRNA16
add: miRNA20; w.in: 0.219; w.bound: 0.218; new synergy: 0.049
add: miRNA17; w.in: 0.373; w.bound: 0.827; new synergy: 0.052
add: miRNA2; w.in: 0.718; w.bound: 1.041; new synergy: 0.074
add: miRNA6; w.in: 1.032; w.bound: 2.376; new synergy: 0.077
add: miRNA18; w.in: 1.913; w.bound: 1.495; new synergy: 0.124
add: miRNA8; w.in: 2.410; w.bound: 1.420; new synergy: 0.135
add: miRNA12; w.in: 3.330; w.bound: 0.500; new synergy: 0.168
Forming new module with seed: miRNA1
add: miRNA19; w.in: 0.375; w.bound: 0.000; new synergy: 0.086
Forming new module with seed: miRNA7
add: miRNA15; w.in: 0.084; w.bound: 0.383; new synergy: 0.019
add: miRNA10; w.in: 0.453; w.bound: 0.398; new synergy: 0.066
add: miRNA14; w.in: 0.736; w.bound: 0.486; new synergy: 0.080
add: miRNA17; w.in: 0.959; w.bound: 0.957; new synergy: 0.080
add: miRNA2; w.in: 1.396; w.bound: 0.986; new synergy: 0.097
Forming new module with seed: miRNA11
add: miRNA3; w.in: 0.122; w.bound: 1.015; new synergy: 0.024
add: miRNA9; w.in: 0.863; w.bound: 0.356; new synergy: 0.120
Forming new module with seed: miRNA5
MRM before merging:
M1 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M2 (synergy=0.14089190465843):
miRNA3 miRNA9
M3 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M4 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M5 (synergy=0.0995481886856942):
miRNA2 miRNA10 miRNA14 miRNA15 miRNA17
M6 (synergy=0.167919254849307):
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20
M7 (synergy=0.0857963527273969):
miRNA1 miRNA19
M8 (synergy=0.0970569736542555):
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17
M9 (synergy=0.119598648023761):
miRNA3 miRNA9 miRNA11
M10 (synergy=0):
miRNA5
Merge cluster threshold: overlap >= 0.80:
MRM after merging/filtering:
M1 (density=3.45e-01; synergy=1.95e-01):
miRNA6 miRNA8 miRNA12 miRNA18
M2 (density=7.35e-01; synergy=1.41e-01):
miRNA3 miRNA9
M3 (density=9.31e-02; synergy=9.71e-02):
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17
M4 (density=1.19e-01; synergy=1.68e-01):
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20
M5 (density=3.75e-01; synergy=8.58e-02):
miRNA1 miRNA19
M6 (density=2.88e-01; synergy=1.2e-01):
miRNA3 miRNA9 miRNA11
Time elapsed for Stage I: 0.030
*Stage II. Grow MRM with mRNA:
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
Mirsynergy
--- call from context ---
gencluster(V, W, H, alpha, density2.tol, verbose)
--- call from argument ---
if (class(H) != "dgCMatrix") H <- Matrix(as.matrix(H))
--- R stacktrace ---
where 1: gencluster(V, W, H, alpha, density2.tol, verbose)
where 2: mirsynergy(W, H, verbose = TRUE)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (V, W, H, alpha, density.tol, verbose)
{
if (!isSymmetric(H)) {
warning(paste("Gene-gene interaction must be symmetric!",
"Upper triangle matrix of H is used.", sep = "\n"))
H[lower.tri(H)] <- t(H)[lower.tri(t(H))]
diag(H) <- 0
}
if (class(H) != "dgCMatrix")
H <- Matrix(as.matrix(H))
N <- as.numeric(nrow(H))
M <- as.numeric(ncol(W))
W2 <- rbind(cbind(H, W), cbind(t(W), Matrix(0, nrow = M,
ncol = M)))
original.id <- rownames(W2)
names(original.id) <- 1:nrow(W2)
dimnames(W2) <- list(1:nrow(W2), 1:ncol(W2))
w.sum <- as.numeric(apply(W2, 1, sum))
tmp <- as.matrix(W2)
n.list <- mclapply(as.numeric(rownames(W2)), function(i) as.numeric(which(tmp[i,
] > 0)))
V2 <- mclapply(V, function(v.t) {
if (verbose)
message(sprintf("\nForming new module with seed: %s",
paste(original.id[v.t$v.in + N], collapse = ",")))
v.t <- init_v(v.t, N, w.sum, n.list, alpha)
mirID <- v.t$v.in
v.t.old <- list()
m <- length(v.t$v.in)
while (!identical(v.t, v.t.old)) {
v.t.old <- v.t
v.t <- grow_v(v.t, W2, w.sum, n.list, alpha, verbose,
original.id, TRUE, N)
}
v.t$miRNA <- original.id[mirID]
idx <- binary_search(v.t$v.in, N)
v.t$mRNA <- original.id[v.t$v.in[1:idx]]
v.t$v.in <- original.id[v.t$v.in]
v.t$v.bound <- original.id[v.t$v.bound]
v.t$card.m <- m
v.t$card.t <- v.t$card
v.t$card <- v.t$card.m + v.t$card.t
v.t$density <- get_density2(v.t)
v.t
})
V2[sapply(V2, function(v) v$density < density.tol)] <- NULL
V2
}
<bytecode: 0x0a7220b8>
<environment: namespace:Mirsynergy>
--- function search by body ---
Function gencluster in namespace Mirsynergy has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
** running examples for arch 'x64' ... ERROR
Running examples in 'Mirsynergy-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mirsynergy
> ### Title: Detect synergistic miRNA regulatory modules by overlapping
> ### neighbourhood expansion
> ### Aliases: mirsynergy
> ### Keywords: clustering microRNA
>
> ### ** Examples
>
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==> Define data, use random,
> ##-- or do help(data=index) for the standard data sets.
> ##
> # simulate N mRNA and M miRNA and their interaction matrices
> load(system.file("extdata/toy_modules.RData", package="Mirsynergy"))
>
> # run mirsynergy clustering
> V <- mirsynergy(W, H, verbose=TRUE)
Discard row/column of all zeros in W
*Stage I. Cluster 18 miRNA:
Forming new module with seed: miRNA6
add: miRNA18; w.in: 0.655; w.bound: 1.535; new synergy: 0.106
add: miRNA8; w.in: 1.152; w.bound: 1.460; new synergy: 0.134
add: miRNA12; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA3
add: miRNA9; w.in: 0.735; w.bound: 0.484; new synergy: 0.141
Forming new module with seed: miRNA17
add: miRNA2; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA2
add: miRNA17; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA10
add: miRNA15; w.in: 0.304; w.bound: 0.532; new synergy: 0.063
add: miRNA14; w.in: 0.573; w.bound: 0.649; new synergy: 0.079
add: miRNA17; w.in: 0.796; w.bound: 1.120; new synergy: 0.080
add: miRNA2; w.in: 1.233; w.bound: 1.149; new synergy: 0.100
Forming new module with seed: miRNA16
add: miRNA20; w.in: 0.219; w.bound: 0.218; new synergy: 0.049
add: miRNA17; w.in: 0.373; w.bound: 0.827; new synergy: 0.052
add: miRNA2; w.in: 0.718; w.bound: 1.041; new synergy: 0.074
add: miRNA6; w.in: 1.032; w.bound: 2.376; new synergy: 0.077
add: miRNA18; w.in: 1.913; w.bound: 1.495; new synergy: 0.124
add: miRNA8; w.in: 2.410; w.bound: 1.420; new synergy: 0.135
add: miRNA12; w.in: 3.330; w.bound: 0.500; new synergy: 0.168
Forming new module with seed: miRNA1
add: miRNA19; w.in: 0.375; w.bound: 0.000; new synergy: 0.086
Forming new module with seed: miRNA7
add: miRNA15; w.in: 0.084; w.bound: 0.383; new synergy: 0.019
add: miRNA10; w.in: 0.453; w.bound: 0.398; new synergy: 0.066
add: miRNA14; w.in: 0.736; w.bound: 0.486; new synergy: 0.080
add: miRNA17; w.in: 0.959; w.bound: 0.957; new synergy: 0.080
add: miRNA2; w.in: 1.396; w.bound: 0.986; new synergy: 0.097
Forming new module with seed: miRNA11
add: miRNA3; w.in: 0.122; w.bound: 1.015; new synergy: 0.024
add: miRNA9; w.in: 0.863; w.bound: 0.356; new synergy: 0.120
Forming new module with seed: miRNA5
MRM before merging:
M1 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M2 (synergy=0.14089190465843):
miRNA3 miRNA9
M3 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M4 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M5 (synergy=0.0995481886856942):
miRNA2 miRNA10 miRNA14 miRNA15 miRNA17
M6 (synergy=0.167919254849307):
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20
M7 (synergy=0.0857963527273969):
miRNA1 miRNA19
M8 (synergy=0.0970569736542555):
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17
M9 (synergy=0.119598648023761):
miRNA3 miRNA9 miRNA11
M10 (synergy=0):
miRNA5
Merge cluster threshold: overlap >= 0.80:
MRM after merging/filtering:
M1 (density=3.45e-01; synergy=1.95e-01):
miRNA6 miRNA8 miRNA12 miRNA18
M2 (density=7.35e-01; synergy=1.41e-01):
miRNA3 miRNA9
M3 (density=9.31e-02; synergy=9.71e-02):
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17
M4 (density=1.19e-01; synergy=1.68e-01):
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20
M5 (density=3.75e-01; synergy=8.58e-02):
miRNA1 miRNA19
M6 (density=2.88e-01; synergy=1.2e-01):
miRNA3 miRNA9 miRNA11
Time elapsed for Stage I: 0.030
*Stage II. Grow MRM with mRNA:
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
Mirsynergy
--- call from context ---
gencluster(V, W, H, alpha, density2.tol, verbose)
--- call from argument ---
if (class(H) != "dgCMatrix") H <- Matrix(as.matrix(H))
--- R stacktrace ---
where 1: gencluster(V, W, H, alpha, density2.tol, verbose)
where 2: mirsynergy(W, H, verbose = TRUE)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (V, W, H, alpha, density.tol, verbose)
{
if (!isSymmetric(H)) {
warning(paste("Gene-gene interaction must be symmetric!",
"Upper triangle matrix of H is used.", sep = "\n"))
H[lower.tri(H)] <- t(H)[lower.tri(t(H))]
diag(H) <- 0
}
if (class(H) != "dgCMatrix")
H <- Matrix(as.matrix(H))
N <- as.numeric(nrow(H))
M <- as.numeric(ncol(W))
W2 <- rbind(cbind(H, W), cbind(t(W), Matrix(0, nrow = M,
ncol = M)))
original.id <- rownames(W2)
names(original.id) <- 1:nrow(W2)
dimnames(W2) <- list(1:nrow(W2), 1:ncol(W2))
w.sum <- as.numeric(apply(W2, 1, sum))
tmp <- as.matrix(W2)
n.list <- mclapply(as.numeric(rownames(W2)), function(i) as.numeric(which(tmp[i,
] > 0)))
V2 <- mclapply(V, function(v.t) {
if (verbose)
message(sprintf("\nForming new module with seed: %s",
paste(original.id[v.t$v.in + N], collapse = ",")))
v.t <- init_v(v.t, N, w.sum, n.list, alpha)
mirID <- v.t$v.in
v.t.old <- list()
m <- length(v.t$v.in)
while (!identical(v.t, v.t.old)) {
v.t.old <- v.t
v.t <- grow_v(v.t, W2, w.sum, n.list, alpha, verbose,
original.id, TRUE, N)
}
v.t$miRNA <- original.id[mirID]
idx <- binary_search(v.t$v.in, N)
v.t$mRNA <- original.id[v.t$v.in[1:idx]]
v.t$v.in <- original.id[v.t$v.in]
v.t$v.bound <- original.id[v.t$v.bound]
v.t$card.m <- m
v.t$card.t <- v.t$card
v.t$card <- v.t$card.m + v.t$card.t
v.t$density <- get_density2(v.t)
v.t
})
V2[sapply(V2, function(v) v$density < density.tol)] <- NULL
V2
}
<bytecode: 0x0000000010200720>
<environment: namespace:Mirsynergy>
--- function search by body ---
Function gencluster in namespace Mirsynergy has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
v.t$card.t <- v.t$card
v.t$card <- v.t$card.m + v.t$card.t
v.t$density <- get_density2(v.t)
v.t
})
V2[sapply(V2, function(v) v$density < density.tol)] <- NULL
V2
}
<bytecode: 0x08e38108>
<environment: namespace:Mirsynergy>
--- function search by body ---
Function gencluster in namespace Mirsynergy has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
** running tests for arch 'x64' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
v.t$card.t <- v.t$card
v.t$card <- v.t$card.m + v.t$card.t
v.t$density <- get_density2(v.t)
v.t
})
V2[sapply(V2, function(v) v$density < density.tol)] <- NULL
V2
}
<bytecode: 0x000000000d53d260>
<environment: namespace:Mirsynergy>
--- function search by body ---
Function gencluster in namespace Mirsynergy has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
* 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: 4 ERRORs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/Mirsynergy.Rcheck/00check.log'
for details.
Mirsynergy.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Mirsynergy_1.24.0.tar.gz && rm -rf Mirsynergy.buildbin-libdir && mkdir Mirsynergy.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Mirsynergy.buildbin-libdir Mirsynergy_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Mirsynergy_1.24.0.zip && rm Mirsynergy_1.24.0.tar.gz Mirsynergy_1.24.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 439k 100 439k 0 0 6307k 0 --:--:-- --:--:-- --:--:-- 6979k
install for i386
* installing *source* package 'Mirsynergy' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Mirsynergy'
finding HTML links ... done
Mirsynergy-package html
mirsynergy html
plot_module_summary html
plot_modules html
print_modules2 html
summary_modules html
tabular_module html
tcga_brca_testdata html
toy_modules html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Mirsynergy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Mirsynergy' as Mirsynergy_1.24.0.zip
* DONE (Mirsynergy)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Mirsynergy' successfully unpacked and MD5 sums checked
|
Mirsynergy.Rcheck/tests_i386/runTests.Rout.fail
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("Mirsynergy")
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Discard row/column of all zeros in W
*Stage I. Cluster 18 miRNA:
Forming new module with seed: miRNA6
add: miRNA18; w.in: 0.655; w.bound: 1.535; new synergy: 0.106
add: miRNA8; w.in: 1.152; w.bound: 1.460; new synergy: 0.134
add: miRNA12; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA3
add: miRNA9; w.in: 0.735; w.bound: 0.484; new synergy: 0.141
Forming new module with seed: miRNA17
add: miRNA2; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA2
add: miRNA17; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA10
add: miRNA15; w.in: 0.304; w.bound: 0.532; new synergy: 0.063
add: miRNA14; w.in: 0.573; w.bound: 0.649; new synergy: 0.079
add: miRNA17; w.in: 0.796; w.bound: 1.120; new synergy: 0.080
add: miRNA2; w.in: 1.233; w.bound: 1.149; new synergy: 0.100
Forming new module with seed: miRNA16
add: miRNA20; w.in: 0.219; w.bound: 0.218; new synergy: 0.049
add: miRNA17; w.in: 0.373; w.bound: 0.827; new synergy: 0.052
add: miRNA2; w.in: 0.718; w.bound: 1.041; new synergy: 0.074
add: miRNA6; w.in: 1.032; w.bound: 2.376; new synergy: 0.077
add: miRNA18; w.in: 1.913; w.bound: 1.495; new synergy: 0.124
add: miRNA8; w.in: 2.410; w.bound: 1.420; new synergy: 0.135
add: miRNA12; w.in: 3.330; w.bound: 0.500; new synergy: 0.168
Forming new module with seed: miRNA1
add: miRNA19; w.in: 0.375; w.bound: 0.000; new synergy: 0.086
Forming new module with seed: miRNA7
add: miRNA15; w.in: 0.084; w.bound: 0.383; new synergy: 0.019
add: miRNA10; w.in: 0.453; w.bound: 0.398; new synergy: 0.066
add: miRNA14; w.in: 0.736; w.bound: 0.486; new synergy: 0.080
add: miRNA17; w.in: 0.959; w.bound: 0.957; new synergy: 0.080
add: miRNA2; w.in: 1.396; w.bound: 0.986; new synergy: 0.097
Forming new module with seed: miRNA11
add: miRNA3; w.in: 0.122; w.bound: 1.015; new synergy: 0.024
add: miRNA9; w.in: 0.863; w.bound: 0.356; new synergy: 0.120
Forming new module with seed: miRNA5
MRM before merging:
M1 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M2 (synergy=0.14089190465843):
miRNA3 miRNA9
M3 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M4 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M5 (synergy=0.0995481886856942):
miRNA2 miRNA10 miRNA14 miRNA15 miRNA17
M6 (synergy=0.167919254849307):
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20
M7 (synergy=0.0857963527273969):
miRNA1 miRNA19
M8 (synergy=0.0970569736542555):
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17
M9 (synergy=0.119598648023761):
miRNA3 miRNA9 miRNA11
M10 (synergy=0):
miRNA5
Merge cluster threshold: overlap >= 0.80:
MRM after merging/filtering:
M1 (density=3.45e-01; synergy=1.95e-01):
miRNA6 miRNA8 miRNA12 miRNA18
M2 (density=7.35e-01; synergy=1.41e-01):
miRNA3 miRNA9
M3 (density=9.31e-02; synergy=9.71e-02):
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17
M4 (density=1.19e-01; synergy=1.68e-01):
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20
M5 (density=3.75e-01; synergy=8.58e-02):
miRNA1 miRNA19
M6 (density=2.88e-01; synergy=1.2e-01):
miRNA3 miRNA9 miRNA11
Time elapsed for Stage I: 0.050
*Stage II. Grow MRM with mRNA:
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
Mirsynergy
--- call from context ---
gencluster(V, W, H, alpha, density2.tol, verbose)
--- call from argument ---
if (class(H) != "dgCMatrix") H <- Matrix(as.matrix(H))
--- R stacktrace ---
where 1: gencluster(V, W, H, alpha, density2.tol, verbose)
where 2: mirsynergy(W, H, verbose = TRUE)
where 3: func()
where 4: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 8: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 9: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
where 10: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp,
tearDownFunc = .tearDown)
where 11: .sourceTestFile(testFile, testSuite$testFuncRegexp)
where 12: RUnit::runTestSuite(suite)
where 13: BiocGenerics:::testPackage("Mirsynergy")
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (V, W, H, alpha, density.tol, verbose)
{
if (!isSymmetric(H)) {
warning(paste("Gene-gene interaction must be symmetric!",
"Upper triangle matrix of H is used.", sep = "\n"))
H[lower.tri(H)] <- t(H)[lower.tri(t(H))]
diag(H) <- 0
}
if (class(H) != "dgCMatrix")
H <- Matrix(as.matrix(H))
N <- as.numeric(nrow(H))
M <- as.numeric(ncol(W))
W2 <- rbind(cbind(H, W), cbind(t(W), Matrix(0, nrow = M,
ncol = M)))
original.id <- rownames(W2)
names(original.id) <- 1:nrow(W2)
dimnames(W2) <- list(1:nrow(W2), 1:ncol(W2))
w.sum <- as.numeric(apply(W2, 1, sum))
tmp <- as.matrix(W2)
n.list <- mclapply(as.numeric(rownames(W2)), function(i) as.numeric(which(tmp[i,
] > 0)))
V2 <- mclapply(V, function(v.t) {
if (verbose)
message(sprintf("\nForming new module with seed: %s",
paste(original.id[v.t$v.in + N], collapse = ",")))
v.t <- init_v(v.t, N, w.sum, n.list, alpha)
mirID <- v.t$v.in
v.t.old <- list()
m <- length(v.t$v.in)
while (!identical(v.t, v.t.old)) {
v.t.old <- v.t
v.t <- grow_v(v.t, W2, w.sum, n.list, alpha, verbose,
original.id, TRUE, N)
}
v.t$miRNA <- original.id[mirID]
idx <- binary_search(v.t$v.in, N)
v.t$mRNA <- original.id[v.t$v.in[1:idx]]
v.t$v.in <- original.id[v.t$v.in]
v.t$v.bound <- original.id[v.t$v.bound]
v.t$card.m <- m
v.t$card.t <- v.t$card
v.t$card <- v.t$card.m + v.t$card.t
v.t$density <- get_density2(v.t)
v.t
})
V2[sapply(V2, function(v) v$density < density.tol)] <- NULL
V2
}
<bytecode: 0x08e38108>
<environment: namespace:Mirsynergy>
--- function search by body ---
Function gencluster in namespace Mirsynergy has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
|
Mirsynergy.Rcheck/tests_x64/runTests.Rout.fail
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("Mirsynergy")
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Discard row/column of all zeros in W
*Stage I. Cluster 18 miRNA:
Forming new module with seed: miRNA6
add: miRNA18; w.in: 0.655; w.bound: 1.535; new synergy: 0.106
add: miRNA8; w.in: 1.152; w.bound: 1.460; new synergy: 0.134
add: miRNA12; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA3
add: miRNA9; w.in: 0.735; w.bound: 0.484; new synergy: 0.141
Forming new module with seed: miRNA17
add: miRNA2; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA2
add: miRNA17; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195
Forming new module with seed: miRNA10
add: miRNA15; w.in: 0.304; w.bound: 0.532; new synergy: 0.063
add: miRNA14; w.in: 0.573; w.bound: 0.649; new synergy: 0.079
add: miRNA17; w.in: 0.796; w.bound: 1.120; new synergy: 0.080
add: miRNA2; w.in: 1.233; w.bound: 1.149; new synergy: 0.100
Forming new module with seed: miRNA16
add: miRNA20; w.in: 0.219; w.bound: 0.218; new synergy: 0.049
add: miRNA17; w.in: 0.373; w.bound: 0.827; new synergy: 0.052
add: miRNA2; w.in: 0.718; w.bound: 1.041; new synergy: 0.074
add: miRNA6; w.in: 1.032; w.bound: 2.376; new synergy: 0.077
add: miRNA18; w.in: 1.913; w.bound: 1.495; new synergy: 0.124
add: miRNA8; w.in: 2.410; w.bound: 1.420; new synergy: 0.135
add: miRNA12; w.in: 3.330; w.bound: 0.500; new synergy: 0.168
Forming new module with seed: miRNA1
add: miRNA19; w.in: 0.375; w.bound: 0.000; new synergy: 0.086
Forming new module with seed: miRNA7
add: miRNA15; w.in: 0.084; w.bound: 0.383; new synergy: 0.019
add: miRNA10; w.in: 0.453; w.bound: 0.398; new synergy: 0.066
add: miRNA14; w.in: 0.736; w.bound: 0.486; new synergy: 0.080
add: miRNA17; w.in: 0.959; w.bound: 0.957; new synergy: 0.080
add: miRNA2; w.in: 1.396; w.bound: 0.986; new synergy: 0.097
Forming new module with seed: miRNA11
add: miRNA3; w.in: 0.122; w.bound: 1.015; new synergy: 0.024
add: miRNA9; w.in: 0.863; w.bound: 0.356; new synergy: 0.120
Forming new module with seed: miRNA5
MRM before merging:
M1 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M2 (synergy=0.14089190465843):
miRNA3 miRNA9
M3 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M4 (synergy=0.195232383222109):
miRNA6 miRNA8 miRNA12 miRNA18
M5 (synergy=0.0995481886856942):
miRNA2 miRNA10 miRNA14 miRNA15 miRNA17
M6 (synergy=0.167919254849307):
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20
M7 (synergy=0.0857963527273969):
miRNA1 miRNA19
M8 (synergy=0.0970569736542555):
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17
M9 (synergy=0.119598648023761):
miRNA3 miRNA9 miRNA11
M10 (synergy=0):
miRNA5
Merge cluster threshold: overlap >= 0.80:
MRM after merging/filtering:
M1 (density=3.45e-01; synergy=1.95e-01):
miRNA6 miRNA8 miRNA12 miRNA18
M2 (density=7.35e-01; synergy=1.41e-01):
miRNA3 miRNA9
M3 (density=9.31e-02; synergy=9.71e-02):
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17
M4 (density=1.19e-01; synergy=1.68e-01):
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20
M5 (density=3.75e-01; synergy=8.58e-02):
miRNA1 miRNA19
M6 (density=2.88e-01; synergy=1.2e-01):
miRNA3 miRNA9 miRNA11
Time elapsed for Stage I: 0.050
*Stage II. Grow MRM with mRNA:
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
Mirsynergy
--- call from context ---
gencluster(V, W, H, alpha, density2.tol, verbose)
--- call from argument ---
if (class(H) != "dgCMatrix") H <- Matrix(as.matrix(H))
--- R stacktrace ---
where 1: gencluster(V, W, H, alpha, density2.tol, verbose)
where 2: mirsynergy(W, H, verbose = TRUE)
where 3: func()
where 4: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 8: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 9: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
where 10: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp,
tearDownFunc = .tearDown)
where 11: .sourceTestFile(testFile, testSuite$testFuncRegexp)
where 12: RUnit::runTestSuite(suite)
where 13: BiocGenerics:::testPackage("Mirsynergy")
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (V, W, H, alpha, density.tol, verbose)
{
if (!isSymmetric(H)) {
warning(paste("Gene-gene interaction must be symmetric!",
"Upper triangle matrix of H is used.", sep = "\n"))
H[lower.tri(H)] <- t(H)[lower.tri(t(H))]
diag(H) <- 0
}
if (class(H) != "dgCMatrix")
H <- Matrix(as.matrix(H))
N <- as.numeric(nrow(H))
M <- as.numeric(ncol(W))
W2 <- rbind(cbind(H, W), cbind(t(W), Matrix(0, nrow = M,
ncol = M)))
original.id <- rownames(W2)
names(original.id) <- 1:nrow(W2)
dimnames(W2) <- list(1:nrow(W2), 1:ncol(W2))
w.sum <- as.numeric(apply(W2, 1, sum))
tmp <- as.matrix(W2)
n.list <- mclapply(as.numeric(rownames(W2)), function(i) as.numeric(which(tmp[i,
] > 0)))
V2 <- mclapply(V, function(v.t) {
if (verbose)
message(sprintf("\nForming new module with seed: %s",
paste(original.id[v.t$v.in + N], collapse = ",")))
v.t <- init_v(v.t, N, w.sum, n.list, alpha)
mirID <- v.t$v.in
v.t.old <- list()
m <- length(v.t$v.in)
while (!identical(v.t, v.t.old)) {
v.t.old <- v.t
v.t <- grow_v(v.t, W2, w.sum, n.list, alpha, verbose,
original.id, TRUE, N)
}
v.t$miRNA <- original.id[mirID]
idx <- binary_search(v.t$v.in, N)
v.t$mRNA <- original.id[v.t$v.in[1:idx]]
v.t$v.in <- original.id[v.t$v.in]
v.t$v.bound <- original.id[v.t$v.bound]
v.t$card.m <- m
v.t$card.t <- v.t$card
v.t$card <- v.t$card.m + v.t$card.t
v.t$density <- get_density2(v.t)
v.t
})
V2[sapply(V2, function(v) v$density < density.tol)] <- NULL
V2
}
<bytecode: 0x000000000d53d260>
<environment: namespace:Mirsynergy>
--- function search by body ---
Function gencluster in namespace Mirsynergy has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
|
|
Mirsynergy.Rcheck/examples_i386/Mirsynergy-Ex.timings
|
Mirsynergy.Rcheck/examples_x64/Mirsynergy-Ex.timings
|